X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
x proximal_to y iff x is closer to the point of attachment with the body than y.
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion.
X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion.
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.
X intersects_median_plane of iff X crosses the midine plane of Y.
x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front.
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
Relation between occurrents, shares start and end boundaries.
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))
A overlaps B if they share some part in common.
S only_in_taxon T iff: S SubClassOf in_taxon only T
S never_in_taxon T iff: S SubClassOf in_taxon only not T
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage.
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
relation between an artery and the structure is supplies with blood.
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
x adjacent_to y iff: x and y share a boundary
Relation between occurrents, shares a start boundary with.
This relation take from EHDAA2 - precise semantics yet to be defined
Relation between occurrents, shares an end boundary with.
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B.
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH].
One of paired external openings of the nasal chamber.[AAO]
Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]
in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity
we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure
the organ that is specialized for smell and is part of the respiratory system
TODO - distinguish generic olfactory apparatus from nose; we have olfactory organ for the generic organ - add new class 'olfactory structure'?
Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
the clusters of hormone-producing cells that are scattered throughout the pancreas
Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]
Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]
A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)
The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]
An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]
It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic–pituitary–gonadal (HPG) and hypothalamic–pituitary–thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9]
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
lateral part of the basal amygdalar nucleus
nucleus amygdalae basalis, pars lateralis
nucleus amygdaloideus basalis, pars lateralis magnocellularis
pars peripherica; systema nervosum periphericum
The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO].
Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]
In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]
parasympathetic part of autonomic division of nervous system
pars parasympathica divisionis autonomici systematis nervosi
Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
somatic nervous system, somatic division
The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
has developmental contribution from NC in verteberates (UBERONREF:0000002)
pars sympathica divisionis autonomici systematis nervosi
sympathetic part of autonomic division of nervous system
A sub-region of the skin. Note the distinct between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
Structural anatomical relation which holds between each anatomical entity of one to three dimensions and some immaterial anatomical entity of one lower dimension such that the latter demarcates (delimits) the former from its neighborhood.
The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
create a separate class for distributed pancreas, eg cyclostomes?
The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]
The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys
The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
A light sensing organ composed of ommatidia
The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
camera-type eye plus associated structures
An organ that is capable of transducing sensory stimulus to the nervous system.
Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.
one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. The beta-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof. The exact signals that induce the growth of feathers on the skin are not known but it has been found that the transcription factor cDermo-1 induces the growth of feathers on skin and scales on the leg.
Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection
The beta-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof.
Appendage that is used to produce lift for flight through the air.
This class is not monophyletic. See also: GO:0007629
Forelimb that is used to produce lift for flight through the air.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
A lamina propria that is part of a respiratory airway.
obsoleted as it was a grouping class that served no purpose
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
An ovarian follicle that has one layer of granulosa cells.
folliculus ovaricus tertiarius (vesiculosus)
folliculus ovaricus tertiarius (vesiculous)
The fluid surrounding the ovum and granulosa cells in the ovarian follicle..
The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.
Region of ovarian follicle filled with follicular fluid.
A hemopoietic organ found in elasmobranchs. Along with the spleen and special tissue around the gonads, this structure produces red blood cells and it is nestled along the top and bottom of the esophagus.
Found in elasmobranchs (sharks and rays) but with some exceptions.
Phenotype notes: Leydig's organ can be quite large - a 1.6-kilogram (3.5-pound) one was reported from a 1.8-metre (6-foot) long Bluntnose Sixgill Shark (Hexanchus griseus). Structure notes: divided into dorsal and ventral patches, gradation varies between species. Lacks erythroblasts and fat cells[Honma 1983]
Multi-tissue structure composed of enameloid, dentine surrounding a pulp cavity, and bone of attachment anchoring the element into the dermis[VSAO].
Multi-tissue structure composed of enameloid, dentine surrounding a pulp cavity, and bone of attachment anchoring the element into the dermis.[VSAO]
Small outgrowths which cover the skin of many cartilaginous fish including sharks. They are similar in structure to teeth, and teeth may have evolved from denticle-like structures in primitive fish.[citation needed] The placoid scales in sharks are formed of dentine with dermal papillae located in the core. These scales develop from the dermal layer of the skin, which is in contrast to the epidermal development seen the in the elasmoid scales of tetrapods. The shape of denticle varies from species to species and can be used in identification. Studies have found that the denticles create tiny vortices that reduce drag to make swimming more efficient. Denticles also allow sharks to swim silently compared to other fish that generate considerable noise when they ply the water[WP][Wikipedia:Dermal_denticle].
Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone.
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
Dense regular connective tissue that connects muscle to bone[VSAO].
Dense regular connective tissue that connects muscle to bone.[VSAO]
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
* Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP)
Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]
From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]
The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[doi:10.1093/icb/icn065]
MA and EMAPA introduce distinct classes for what appears to be the same thing
A biological tissue mass, most commonly a mass of nerve cell bodies.
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
A ganglion is a cluster of ➞neurons. It is part of a ➞nervous system. It may include ➞glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and ➞neurites are concentrated in the centre of the ganglion to form the ➞neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by ➞connectives or transversally by ➞commissures
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302].
Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com).
eye-spots which may be set into a pit to reduce the angles of light that enters and affects the eyespot, to allow the organism to deduce the angle of incoming light
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
Simple eye that has a small aperture (which may be adjustable) and deep pit. It is only found in the nautiloids.
simple eye that consists of a lens of one refractive index
simple eye that has two or more lenses. Some marine organisms bear more than one lens; for instance the copeopod Pontella has three. The outer has a parabolic surface, countering the effects of spherical aberration while allowing a sharp image to be formed. Copilla's eyes have two lenses, which move in and out like a telescope
The deepest portions of the vagina, extending into the recesses created by the vaginal portion of cervix[WP,unvetted].
A C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM).
An oval area in the retina, usually located temporal to the posterior pole of the eye and slightly below the level of the optic disk. It is characterized by the presence of a yellow pigment diffusely permeating the inner layers, contains the fovea centralis in its center, and provides the best phototopic visual acuity. It is devoid of retinal blood vessels, except in its periphery, and receives nourishment from the choriocapillaris of the choroid. (From Cline et al., Dictionary of Visual Science, 4th ed)
Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified].
this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule
Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO]
A tubular structure that contains, conveys body fluid, such as blood or lymph.
Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
in humans, consists of adventitial, muscular and mucoa layers
the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
A tubular structure that transports or secretes substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball[FMA].
Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA].
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A stage that is part of the embryo stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
Uberon includes clade-specific subclasses, e.g. nematod larva
It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
The pupal stage is found only in holometabolous insects, those that undergo a complete metamorphosis, going through four life stages; embryo, larva, pupa and imago
An organ segment that is part of a respiratory tract [Automatically generated definition].
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO].
ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman’s capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
mixed ectoderm/mesoderm/endoderm-derived structure
The organs associated with producing offspring in the gender that produces spermatozoa.
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney[GO]
By contrast to the pronephros, the histological features of the mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP] comment: Taxon notes: The mesonephros persists and form the permanent kidneys in fishes and amphibians, but in reptiles, birds, and mammals, it atrophies and for the most part disappears rapidly as the permanent kidney (metanephros) begins to develop during the sixth or seventh week. By the beginning of the fifth month only the ducts and a few of the tubules of the mesonephros remain[WP]
In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]
A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
A mass of cells that develop into the body of the embryo and some extraembryonic tissues
A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]
embryoblastus; massa cellularis interna; pluriblastus senior
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]
The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta
Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast]
TODO - consider relationship to UBERON:0000091 ! bilaminar disc
this term groups together disparate structures with different relationships.
A primary germ layer that can give rise to both mesoderm and endoderm.[AAO]
The inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm. Kimmel et al, 1995.[TAO]
In mammal and avian, extraembryonic endoderm such as visceral endoderm and hypoblast play essential roles in the embryonic axis formation and germ layer development. These extraembryonic tissues are generally considered to have been created in ancestral amniotes evolved from the Xenopus-type ancestor (reference 1); The endomesoderm secretes as yet unidentified signals that posteriorize the ectoderm, which would otherwise adopt an anterior fate. Our results point to a conserved function at the base of deuterostomes for beta-catenin in germ layer specification and to a causal link in the definition of the posterior part of the embryonic ectoderm by way of activating posteriorizing endomesodermal factors (reference 2).[well established][VHOG]
fluid-filled central region of a blastocyst.
A blastocoel forms during embryogenesis when a zygote (a fertilized ovum) divides into many cells through mitosis. The blastocoel is the cavity of the blastula, a closed space which is invaded by early mesenchyme and later obliterated by the enlarging archenteron.[AAO]
The cavity inside the blastula. [The_evolution_of_organ_systems_(2007)_Oxford:_Oxford_University_Press, p.150, see_Schmidt-Rhaesa_A][VHOG]
In the development of many animals, a hollow blastula stage is formed during early embryogenesis. Such a hollow blastula is even regarded as an autapomorphy of Metazoa and is present already in some sponges.[well established][VHOG]
A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
A depression or fissure in the surface of an organ.
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]
A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[doi:10.1242/dev.091751].
Structure around the opening into the archenteron during the embryonic stages of an organism. The distinction between protostomes and deuterostomes is based on the direction in which the mouth (stoma) develops in relation to the blastopore.
A slit-like invagination on the dorsal side of the blastula surface of the embryo where the mesoderm and endoderm move inside the embryo at gatrulation.[AAO]
In protostome development, the first opening in development, the blastopore, becomes the animal's mouth; In deuterostome development, the blastopore becomes the animal's anus
A lung lobe is one of the rounded projections that compose the lung[GO].
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
Instant starting or ending a life cycle stage. These can be arbitrary/fiat.
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The stage of being a sexually mature adult animal.
the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin; it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
Primitive gas exchange portion of the lung composed of type I and type II cells[GO].
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represneted by a tree of tubes (see the FMA class)
Structure derived from foregut that becomes a lung[GO].
Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.
Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions.
A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. (Nolte, J., The Human Brain 3rd edition)
Connective tissue surrounding a fascicle[Wikipedia:Perineurium].
consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer)
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
The loose connective tissue within the perineurium that continues into nerve fascicles and surrounds individual fibers. (Nolte, J. The Human Brain 3rd edition)
a layer of delicate connective tissue that encloses the myelin sheath of a nerve fiber within a funiculus[Wikipedia:Endodeurium].
A loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition
outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium].
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO)
Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves
the group of motor neurons residing in the pons that innervate the muscles of facial expression
FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus.
prominent oval structure in the medulla oblongata, present in pairs, the lower portion of the brainstem. They contain the olivary nuclei
Foramen that pierces the transverse processes of the seven cervical vertebrae. In the upper six vertebrae, the foramen gives passage to the vertebral artery, vertebral vein, and a plexus of sympathetic nerves. The seventh foramen lacks the artery, but contains the vein and sympathetic nerves.
foramen transversarium of cervical vertebra
The medial portion of the articular surface of the humerus is named the trochlea, and presents a deep depression between two well-marked borders; it is convex from before backward, concave from side to side, and occupies the anterior, lower, and posterior parts of the extremity. It is directly inferior to the most prominent anterior humeral fossia, the Coronoid fossia. It articulates with the ulna.
Paired fin that is located in the thoracic region of the body.
Paired fin that is located in the thoracic region of the body.[TAO]
Paired fin that is located in the thoracic region of the body.[VSAO]
Paired fin located in the abdominal position of the body.
Paired fin located in the abdominal position of the body.[TAO]
Paired fin located in the abdominal position of the body.[VSAO]
A layer of the ovarian follicle that consists of theca cells.
The theca folliculi are responsible for the production of testosterone from androstenedione in females, and indirectly the production of estrogens by supplying the neighboring granulosa cells with androstenedione that can then be used as a substrate for aromatase. [Wikipedia:Theca_of_follicle]
The theca externa is the outer layers of the theca folliculi. It contains abundant collagen and is mainly supportive.
theca externa (folliculus ovaricus tertiarius)
Theca interna cells express receptors for luteinizing hormone, which when activated will stimulate the production of androstenedione from cholesterol by the enzyme desmolase. Androstenedione ultimately gives the granulosa cells the precursor substrate for estrogen manufacturing.
theca interna (folliculus ovaricus tertiarius)
internal coat of capsule of graafian follicle
The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus.
requires alignment with EHDAA2 and complete developmental relationships
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
Anatomical conduit that connects two adjacent body spaces, surrounded by two or more subdivisions of two or more organs. Examples: right atrioventricular orifice, orifice of artery, hilum of kidney, porta hepatis[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
hindgut endoderm and proctodeal ectoderm.
endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females
The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
An organ segment that is part of a colon [Automatically generated definition].
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
Vomit is a bodily fluid consisting of the expulsed contents of the stomach of an organism disgorged through the mouth or nose.
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
Excreta are bodily fluids consisting of waste matter, such as sweat or feces, discharged from the body.
Pleural effusion is a bodily fluid that is produced in exess and accumulates in the pleural cavity, the fluid-filled space that surrounds the lungs. Excessive amounts of such fluid can impair breathing by limiting the expansion of the lungs during inhalation.
Editor noyes: cede to MPATH? Note the ncit class is under finding.
A bodily fluid secreted from the body via the mouth or nose.
Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells.
Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid).
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
A region of the posterior torso (lower back) beneath the ribs and above the ilium.
The narrow part of the shaft of the radius just below the head.
A ridge on the cerebral cortex. It is generally surrounded by one or more sulci .
A blood brain barrier that is composed of endothelial cells.
A blood brain barrier composed of glial cells.
Dorsal part (roof region) of the telencephalon[GO].
In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume.
In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus
Dorsal part (base region) of the telencephalon.
BTO term refers specifically to the avian structure
A thin protuberance on the surface of the body of an echinoderm containing diverticula of the water vascular system lined by ciliated peritoneum. Along with tube feet, provide the principle gas exchange surfaces..
A gill that develops in the walls of the pharynx along a series of gill slits opening to the exterior. In fish, the gills are located on both sides of the pharynx.
In bony fish, the gills are covered by a bony cover called an operculum. When a fish breathes, it opens its mouth at regular times and draws in a mouthful of water. It then draws the sides of its throat together, forcing the water through the gill openings. The water passes over the gills on the outside. Valves inside the mouth keep the water from escaping through the mouth again. The operculum can be very important in adjusting the pressure of water inside of the pharynx to allow proper ventilation of the gills. Lampreys and sharks lack an operculum, they have multiple gill openings. Also, they must use different methods to force water over the gills. In sharks and rays, this ventilation of the gills is achieved either by the use of spiracles or ram ventilation (ventilation by constantly swimming). Although some animals use this method it is much better for animals to use a spiracle because they are less susceptible to injury
Gills are made of filaments which help increase surface area for oxygen exchange
A chitinous extracellular secretion of the four underlying cone cells and the pigment cells.
the bone forming the forehead and roof of the eye orbit
fused in humans, paired in other animals
In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).
In humans: bone forming side and roof of cranium. Each bone is irregularly quadrilateral in form, and has two surfaces, four borders, and four angles.
The homologization of cranial bones of actinopterygians with those of sarcopterygians based on the bone names established in human anatomy is favored in order to permit the building of phylogenetic relationship schemes beyond the taxonomic boundaries of osteichthyans (including tetrapods). (...) In actinopterygians, the terms parietal and postparietal bones have to replace the commonly used terms 'frontal' and 'parietal' bones for the two paired bones on the skull roof.[well established][VHOG]
The frontal bone in teleost fish is the homolog of the parietal bone in tetrapods[various]. In many non-mammalian tetrapods, they are bordered to the rear by a pair of postparietal bones that may be solely in the roof of the skull, or slope downwards to contribute to the back of the skull, depending on the species. In the living tuatara, and many fossil species, a small opening, the parietal foramen, lies between the two parietal bones. This opening is the location of a third eye in the midline of the skull, which is much smaller than the two main eyes
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.
Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496].
Portion of connective tissue that connects bone or cartilage.[TAO]
Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]
this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament
A specialized claw or nail on the foot of certain primates, used for personal grooming.
A neural arch that is part of a vertebral bone 2.
vertebral foramen of cervical vertebra 2
vertebral foramen of cervical vertebra 1
The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital
A craniometric point on the posterior root of the zygomatic process of the temporal bone directly above the auricular point.
A closed space between the embryo and the amnion which contains the amniotic fluid and is formed by the fusion of the parts of the anterior and posterior amniotic folds.
The closed sac between the embryo and the amnion, containing the amniotic fluid. [Free_Online_Medical_Dictionary]
An adductor muscle that attaches to the hip and femur. In humans, it is a part of the adductor group of the thigh, that as the name suggests adducts the thigh. The adductor longus muscle forms the medial wall of the femoral triangle[WP, generalized].
Originates on the iliac portion of the ventral iliac rim and inserts on the lateral surface of the M. adductor magnus.[AAO]
definition generalized to accommodate AAO class - 'Originates on the iliac portion of the ventral iliac rim and inserts on the lateral surface of the M. adductor magnus.' [AAO:0010034]
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath
TODO - add layer relations. 'tendon sheath' GAT in FMA.
the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected
A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG]
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity.
defined generically to encompass both vertebrates and invertebrates
The upper ventral region of an animal's torso.
The breasts of a female primate’s body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
A muscle that, upon contraction, tends to straighten a joint or limb. The antagonist of a flexor muscle[BTO]. Any of the muscles that increase the angle between members of a limb, as by straightening the elbow or knee or bending the wrist or spine backward. The movement is usually directed backward, with the notable exception of the knee joint. In humans, certain muscles of the hand and foot are named for this function. In the hand these include the extensor carpi radialis brevis, extensor carpi radialis longus, and extensor carpi ulnaris, which run from the humerus (bone of the upper arm) along the back of the forearm to the metacarpal bones at the back of the hand[Britannica]
This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia
A mucosa that is part of a cecum [Automatically generated definition].
intestinum crassum caecum mucosa of organ
intestinum crassum caecum mucous membrane
mucosa of organ of intestinum crassum caecum
mucous membrane of intestinum crassum caecum
organ mucosa of intestinum crassum caecum
The space between the arachnoid and pia mater.
A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells.
The cytotrophoblast (or layer of Langhans) is the inner layer of the trophoblast, interior to the syncytiotrophoblast in an embryo. It serves to anchor the embryonic chorion to the maternal endometrium. Cytotrophoblasts are stem cells in the chorionic villi. During differentiation, mononuclear cytotrophoblast fuse together into the multinucleated syncytiotrophoblasts. The primary villi has only the cytotrophoblast as an axe. [WP,unvetted].
todo - unify with EHDAA2, which distinguishes multiple types of cytotrophoblast
A derivative layer of the trophoblast, the cells of which retain their boundaries and contribute to the extraembryonic mesoderm [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.189, see_Kardong_KV][VHOG]
A mucosa that is part of a duodenum [Automatically generated definition].
TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.
Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].
Any of the branched tubules in the inner lining of the stomach that secrete gastric juice and protective mucus.
Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
We model the digestive tract as consisting of two parts: the wall and the lumen.
The enlarged basal part of a hair within the skin[BTO]. The root of the hair ends in an enlargement, the hair bulb, which is whiter in color and softer in texture than the shaft, and is lodged in a follicular involution of the epidermis called the hair follicle. [Wikipedia].
A mucosa that is part of a ileum [Automatically generated definition].
bone marrow in which the fat cells predominate in the meshes of the reticular network.
A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
Note that some sources treat 'intestinal gland' as synonymous with crypts
In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
The hyoid bone and the clavicle are the only bones located in the throat of mammals.
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
A dielectric (electrically insulating) material consisting of protein and fat that forms a layer, the myelin sheath, usually around only the axon of a neuron. Myelin is about 40 % water; the dry mass of myelin is about 70 - 85 % lipids and about 15 - 30 % proteins. Some of the proteins that make up myelin are myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), and proteolipid protein (PLP). The primary lipid of myelin is a glycolipid called galactocerebroside (GalC). The intertwining hydrocarbon chains of sphingomyelin serve to strengthen the myelin sheath.
myelinated plasma membrane of Schwann cell
BTO has def The multilamellar myelin membrane is a specisalised lipid-rich domain of the glial cell plasma membrane. FMA has primary term name Myelinated plasma membrane of Schwann cell
The insulating envelope that surrounds nerve fibers or axons.
do not cede to GO until GO includes has_part link to myelin
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead.
Sensory medial ramus of the trigeminal nerve.[AAO]
The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]
ophthalmic division of fifth cranial nerve
ophthalmic division of trigeminal nerve (V1)
ophthalmic division of trigeminal nerve (Va)
Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html]
A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex].
obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]
A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae.
As it is required for running, not all animals have a nuchal ligament
functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
A mucosa that is part of a pharynx [Automatically generated definition].
The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)
A aired, lobulated, modified sebaceous glands located in the inguinal region adjacent to the penis and vagina, with pheromonal functions in male rodents; in males, the preputial gland empties into the preputial cavity and in females, the preputial (aka clitoral) gland duct empties into the clitoral fossa.
the paired, lobulated, modified sebaceous glands of the corona, the neck of the glans penis, and the inner surface of the prepuce with pheromonal functions in male rodents; male preputial secretions strongly attract females, may accelerate estrus, and have been implicated in intermale aggression; homologous to the clitoral glands (aka female preputial glands) in female rodents; there is no true anatomical equivalent in humans.
There is debate about whether humans have functional homologues to preputial glands.
The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
the inner portion of the kidney consisting of the renal pyramids
The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water
A part of the immune system that consists of the phagocytic cells located in reticular connective tissue. The cells are primarily monocytes and macrophages, and they accumulate in lymph nodes and the spleen. The Kupffer cells of the liver and tissue histiocytes are also part of the RES[WP].
An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
consider merging with transitional epithelium. MA uses the label 'urothelium' exclusively. FMA uses 'transitional epithelium' and has 'urothelium' as a sibling. FMA also lists 'urothelium' as the only example of 'transitional epithelium'. MP treats them differently
A muscle that when contracted acts to bend a joint or limb in the body.
A muscle that decreases the angle of a joint.[TAO]
The adductor brevis is a muscle in the thigh situated immediately behind the pectineus and adductor longus. It is somewhat triangular in form, and arises by a narrow origin from the outer surfaces of the superior and inferior rami of the pubis, between the gracilis and obturator externus. Its fibers, passing backward, lateralward, and downward, are inserted, by an aponeurosis, into the line leading from the lesser trochanter to the linea aspera and into the upper part of the linea aspera, immediately behind the pectineus and upper part of the adductor longus.[WP].
The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP].
Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]
The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]
* According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
An adductor muscle that attaches to the pelvic bone and the femur. In humans, the adductor magnus is a large triangular muscle, situated on the medial side of the thigh. The portion which arises from the ischiopubic ramus (a small part of the inferior ramus of the pubis, and the inferior ramus of the ischium) is called the 'adductor magnesius portion', and the portion arising from the tuberosity of the ischium is called the 'hamstring portion'. The hamstring portion is not considered part of the hamstring group of muscles, but it is adjacent to it.[WP,generalized].
Origin by two heads that are separated by a ventral tendon of the M. semitendinosus. One head originates from the ventral border of the pubic portion of the pelvic rim. The other head originates from the ischiatic border of the pelvic rim. The ventral head fuses with accessory head from the M. semitendinosus and inserts along the ventro-medial border of the femur. The dorsal belly merges with the ventral and accessory heads and inserts along the medial surface of the femur.[AAO]
Definition generalized to accommodate AAO class - 'Origin by two heads that are separated by a ventral tendon of the M. semitendinosus. One head originates from the ventral border of the pubic portion of the pelvic rim. The other head originates from the ischiatic border of the pelvic rim. The ventral head fuses with accessory head from the M. semitendinosus and inserts along the ventro-medial border of the femur. The dorsal belly merges with the ventral and accessory heads and inserts along the medial surface of the femur.' [AAO:0010040]
extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated).
A muscle on the upper surface of the foot that helps extend digits 2 through 4.
On either side of the corpus collosum, the fibers radiate in the white substance and pass to the various parts of the cerebral cortex; those curving forward from the genu into the frontal lobe constitute the forceps anterior, and those curving backward into the occipital lobe, the forceps posterior. Between these two parts is the main body of the fibers which constitute the tapetum and extend laterally on either side into the temporal lobe, and cover in the central part of the lateral ventricle. [Wikipedia via Greys]
not to be confused with BTO:0001350 or GO:0048655-tapetal layer morphogenesis
The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini.
mandibular division of fifth cranial nerve
mandibular division of trigeminal nerve [Vc; V3]
The part of the hindlimb between pelvis and the knee, corresponding to the femur.
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
Naming conventions for pod terms under discussion within phenoscape group.
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
Medial ramus (sensory) of the trigeminal nerve.[AAO]
relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
maxillary division of fifth cranial nerve
maxillary division of trigeminal nerve (Vb; V2)
A mucosa that is part of a respiratory airway.
undefined in FMA. BTO and MIAA refers to plant structure only
bundles of smooth muscle fibers forming the muscular wall of the urinary bladder, which are arranged in a longitudinal and a circular layer and, on contraction, serve to expel urine[MP].
muscularis propria of the urinary bladder
Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP].
A note of confusion is the difference between apocrine secretion and apocrine sweat gland. Apocrine secretion refers to the apical loss of a cell's membrane to create cell blebs, thus creating a secretory product. Apocrine sweat gland refers to a structure, not a secretion process. Apocrine sweat glands actually use a merocrine type secretion, or that mediated by exocytosis of secretory granules. When 'apocrine gland' is used without the word sweat, it is often referring to the gland which uses merocrine secretion, and not the secretion method. The important difference in apocrine sweat gland structure is its larger lumen, compared to the more narrow lumen of the eccrine sweat gland.
In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region.
Anatomical system that consists of all the muscles of the body[VSAO, modified].
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
the label 'labial gland' refers to two distinct classes. From the BTO def: 1. One of the small tubular mucous and serous glands lying beneath the mucous membrane of the lips.n2. A salivary gland, or modification thereof, opening at the base of the labium in certain insects.
crescent-shaped fibrocartilaginous structure present in the knee, acromioclavicular, sternoclavicular, and temporomandibular joints[2] that, in contrast to articular disks, only partly divides a joint cavity.[3] A small meniscus also occurs in the radio-carpal joint.
A part of the pharynx that consists of a flap of elastic cartilage tissue plus a mucous membrane covering, attached to the entrance of the larynx. The epiglottis is found at the root of the tongue and folds back over the entrance to the larynx during swallowing, preventing inhalation of food or drink[MP,modified]
The core of the crystalline lens, surrounded by the cortex.
in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular
The longissimus is the muscle lateral to the semispinalis. It is the longest subdivision of the sacrospinalis that extends forward into the transverse processes of the posterior cervical vertebrae. [WP,unvetted].
The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus.
in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems
cochlear part of vestibulocochlear ganglion
vestibulocochlear VIII ganglion cochlear component
vestibulocochlear ganglion cochlear component
Any of the large papillae, which have multiple taste buds in the trough surrounding the papillae, located near the base and on the dorsal side of the tongue
Any one of the largest papilla of the tongue, 8 to 12 in number, arranged in the form of a V anterior to the sulcus terminalis of the tongu[BTO:0001705, http://en.wikipedia.org/wiki/Vallate_papilla]e
An epithelium that is part of a colon [Automatically generated definition].
Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]
Any portion of cartilage tissue that is part of the sternum
Examples: cartilage of manubrium, cartilage of xiphoid process
A mucosa that is part of a jejunum [Automatically generated definition].
An epithelium that is part of a jejunum.
the upturned perpendicular extremity of the mandible
The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted].
The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL).
One of a a paired bundle of nerve fibers plus ganglia that run from the base of the skull to the coccyx.
Any of a group of sympathetic ganglia which form two chains extending from the base of the skull to the coccyx along the sides of the spinal column.
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A mucosa that is part of a bronchus [Automatically generated definition].
the part of the cerebral cortex responsible for processing visual information.
The visual cortex is made up of Brodmann area 17 (the primary visual cortex), and Brodmann area 18 and Brodmann area 19, the extrastriate cortical areas.
A small, nipple-like interdigitation of the dermis into the epidermis.
consider adding grouping class for TAO:0001995 ! papilla
In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints)
Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells.
ncit has 'hair papilla' as part of hypodermis
A gland in which the principal secretory cells are mucus secreting cells.
In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
An anatomical wall that is part of an artery [Automatically generated definition].
A narrow fluid-containing space, often only a potential space, between the dura mater and the arachnoid.
consider obsoleting - see http://www.ncbi.nlm.nih.gov/pubmed/8421539
An epithelium consisting of myopethelial cells, which are contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament[CL].
A merocrine, unbranched, unbranched, coiled, tubular gland sweat gland. In humans, distributed over almost all of the body surface, and promote cooling by evaporation of their secretion.
in mice, found only on footpads; in humans, entire body including soles and palms
Gastric pits are indentations in the stomach which denote entrances to the gastric glands. They are deeper in the pylorus than they are in the other parts of the stomach. The human stomach has several million of these pits.
The outermost layer of trophoblast, produced by cytotrophoblast where there is direct contact with maternal decidua rather than blood. The EVT cells travel into the decidua, reacting with NK cells and invading maternal blood vessels feeding the placenta, softening the walls and replacing the lining with fetal tissue, a process called conversion.
A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies.
A nucleus medially located within the ventral nuclei of the thalamus.
ventral intermediate nucleus of thalamus
A group of nuclei located in the medial portion of the ventral thalamic nuclei.
set of ventral medial nuclei of thalamus
A portion of the nucleus of ansa lenticularis located medial to the posterior limb of the internal capsule, along the course of the ansa lenticularis and the inferior thalamic peduncle or as a separate nucleus within the internal capsule adjacent to the medial GLOBUS PALLIDUS (NeuroNames, http://rprcsgi.rprc. washington.edu/neuronames/ (September 28, 1998)). In non-primates, the entopeduncular nucleus is analogous to both the medial globus pallidus and the entopeduncular nucleus of human.
The term entopeduncular nucleus in human neuroanatomy refers to a portion of the nucleus of the ansa lenticularis described variously as located medial to the posterior limb of the internal capsule ( Riley-1943 ), along the course of the ansa lenticularis and the inferior thalamic peduncle ( Crosby-1962 ), or as a separate nucleus within the internal capsule adjacent to the medial segment of the globus pallidus ( Nomina-1983 ).[NN]
The posterior of the two nuclei paraventriculares thalami.
dorsal paraventricular nucleus of thalamus
nucleus paraventricularis posterior thalami
posterior paraventricular nucleus of thalamus
posterior paraventricular nucleus of the thalamus
The anterior of the two nuclei paraventriculares thalami.
ventral paraventricular nucleus of thalamus
anterior paraventricular nucleus of thalamus
anterior paraventricular nucleus of the thalamus
anterior periventricular nucleus of the hypothalamus
nucleus paraventricularis anterior thalami
periventricular hypothalamic nucleus, anterior part
Nerve cell nuclei situated ventrally in the intermediate hypothalamic region, mainly in the lateral hypothalamic area.
The arachnoid barrier layer is a part of the arachnoid meningeal layer. It is formed by tight junctions between the endothelial cells of cerebral capillaries in the arachnoid mater.
The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges.
A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP].
A vein that drains the left pampiniform plexus and empties into the left renal vein.
A vein that drains the right pampiniform plexus and empties into the inferior vena cava.
introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle'
The habenular trigone is a small depressed triangular area situated in front of the superior colliculus and on the lateral aspect of the posterior part of the taenia thalami. It contains a group of nerve cells termed the ganglion habenulC&. Fibers enter it from the stalk of the pineal body, and others, forming what is termed the habenular commissure, pass across the middle line to the corresponding ganglion of the opposite side. Most of its fibers are, however, directed downward and form a bundle, the fasciculus retroflexus of Meynert, which passes medial to the red nucleus, and, after decussating with the corresponding fasciculus of the opposite side, ends in the interpeduncular ganglion.
superclass in BTO is thalamic nucleus, not present in most ontologies
Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996).
Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842].
White fibrous tissue that replaces the regressing corpus luteum in the human ovary in the latter half of pregnancy, or soon after ovulation when pregnancy does not supervene.
The anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas.nnThis brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals.nnThe most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes).nnMany authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. - definition adapted from Wikipedia
Area of uterine endometrium found between the implanted chorionic vesicle and the myometrium.
As the embryo enlarges, the decidua capsularis becomes stretched and smooth. Eventually the decidua capsularis merges with the decidua parietalis, obliterating the uterine cavity
The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain.
Body substance in a liquid or semisolid state produced by an exocrine gland. Example: saliva, sebum, blood, plasma, semen, urine.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Cavernous branch of cavernous part of internal carotid artery
ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)
1. The mucous membrane lining the canal of the cervix uteri. 2. The region of the opening of the uterine cervix into the uterine cavity.
An anatomical wall that is part of a uterus [Automatically generated definition].
the paired glands located slightly posterior and to the left and right of the opening of the vagina in the superficial perineal pouch in females; they secrete mucus to lubricate the vagina and are homologous to bulbourethral (Cowper's) glands in males
resolve difference in WP vs MP, superficial vs deep perineal pouch
Small mucous glands opening upon the vestibular mucous membrane between the urethral and the vaginal orifice.
check and part_of relationships to mammalian vulva / urethra
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia].
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Anatomical structure that is a direct part of the cell.
TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO
Multi-tissue structure that is part of a compound organ.
Curator notes: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
Multi-tissue structure that is not part of a compound organ.
A gonad of a male animal. A gonad produces and releases sperm.
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
The organs and associated structures associated with bearing offspring in a female animal.
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
see also conceptus extraembryonic component in EHDAA2.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.
Will be obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue.
this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell.
A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon.[well established][VHOG]
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Epithelium that consists of epithelial cells not arranged in one ore more layers.
Compound organ that contains one or more macroscopic anatomical spaces.
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
Compound organ that does not contain macroscopic anatomical spaces.
Curator notes: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future. Note also that we place the FMA class 'solid organ' here, and the FMA includes many glands plus the liver as solid organs, which some may find confusing
The ileocecal valve is a sphincter muscle situated at the junction of the small intestine (ileum) and the large intestine. Its critical function is to limit the reflux of colonic contents into the ileum.
A thin muscle connecting the junction between the duodenum, jejunum, and duodenojejunal flexure to connective tissue surrounding the superior mesenteric artery and coeliac artery
A muscle that arises from the lower half of the ligamentum nuchæ, from the spinous process of the seventh cervical vertebra, and from the spinous processes of the upper three or four thoracic vertebræ and inserts the mastoid process of the temporal bone, and into the rough surface on the occipital bone just below the lateral third of the superior nuchal line[WP,modified].
Extend, rotate, and laterally flex the head
the triangular subcallosal plate of commissural fibers resulting from the converging of the right and left fornix bundles which exchange numerous fibers and which curve back in the contralateral fornix to end in the hippocampus of the opposite side
This class was created automatically from a combination of ontologies
A semifluid mass of partly digested food expelled by the stomach into the duodenum.
Chyme has a low pH that is countered by the production of bile, helping to further digest food. Chyme is also part liquid and part solid: a thick semifluid mass of partially digested food and digestive secretions that is formed in the stomach and intestine during digestion.
Chyle is a bodily fluid consisting of a milky fluid consisting of lymph and emulsified fats; formed in the small intestine during digestion of ingested fats.
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
One of the repeated divisions of the whole organism.
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
The nutritive substance contained in the egg.
A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish [GO].
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[UBERONREF:0000002]
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
A double row of cells which are located at the midline from the end of gastrulations. The morphology of these cells is distinct from adjacent ectodermal cells - they are elongated such that one end remains exposed to the outside of the embryo at the mideline while the other end bissects the internalised mesoderm.
Split term? The part of the mesenchyme derived from ectoderm, especially from the embryonic neural crest from which the pigment cells, meninges, and most of the branchial cartilages develop.[TFD]
Motor nerve of the pharynx, arises from the upper part of the ganglion nodosum, and consists principally of filaments from the cranial portion of the accessory nerve.
pharyngeal branch of inferior vagal ganglion
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage[ZFA]. A proctodeum is the back ectodermal part of an alimentary canal. It is created during embryogenesis by a folding of the outer body wall[WP].
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
originally unified on basis of terminological similarity
A muscle that acts on the pharynx[WP, vetted].
A pharyngeal muscle is any muscle that forms part of the pharynx[GO].
Innervation notes: They are innervated by the pharyngeal branch of the Vagus nerve (CN X) with the exception of the stylopharyngeus muscle which is innervated by the glossopharyngeal nerve (CN IX).[WP]
The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO].
The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects.
A bundle of myelinated nerve fibers passing transversely through the lamina terminalis and connecting symmetrical parts of the two cerebral hemispheres; it consists of a smaller anterior part (pars anterior commissurae anterioris) and a larger posterior part (pars posterior commissurae anterioris).
In all vertebrates the thin structure that connects the two halves of the telencephalon shows a ridge-like thickening at the basal side known as the anterior commissure.[well established][VHOG]
Rounded band of white fibers crossing the middle line on the dorsal aspect of the upper end of the cerebral aqueduct. It is important in the bilateral pupillary light reflex. Its fibers acquire their medullary sheaths early, but their connections have not been definitely determined. Most of them have their origin in a nucleus, the nucleus of the posterior commissure (nucleus of Darkschewitsch), which lies in the central gray substance of the upper end of the cerebral aqueduct, in front of the nucleus of the oculomotor nerve. Some are probably derived from the posterior part of the thalamus and from the superior colliculus, whereas others are believed to be continued downward into the medial longitudinal fasciculus. The posterior commissure interconnects the pretectal nuclei, mediating the consensual pupillary light reflex[WP]. Diencephalic tract which is located in the vicinity of the dorsal diencephalon and mesencephalon and connects the pretectal nuclei. From Neuroanatomy of the Zebrafish Brain[ZFA].
add connects relationships and check these outside mammalia
part_of brainstem in MA; midbrain tectum in NIF
obsoleted because inconsistencies arise due to ZFA term being both embryonic and extraembryonic
one of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation.
Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN10:0471888893]
A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]
(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon
The frontal nerve is the largest branch of the ophthalmic, and may be regarded, both from its size and direction, as the continuation of the nerve. It enters the orbit through the supraorbital foramen, and runs forward between the Levator palpebræ superioris and the periosteum. Midway between the apex and base of the orbit it divides into two branches, supratrochlear nerve and supraorbital nerve. [WP,unvetted].
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
the membranous folds of the heart that prevent reflux of fluid
One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]
Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]
Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation
This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
The most superficial muscle on the medial side of the thigh. It is thin and flattened, broad above, narrow and tapering below. It arises by a thin aponeurosis from the anterior margins of the lower half of the symphysis pubis and the upper half of the pubic arch.
AAO has minor and major gracilis, which merge together, attaching the pelvic rim to the tibiofibula - this could be grouped with the mammalian gracilis at some level; note the current insertion site is 'tibia' which would be modified for amphibian tibiafibula
Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column.
obsoleted as it conflated a generic functional grouping with a specific group of muscles in the leg/hip
GO uses visceral and smooth interchangeably
intestinal muscle cell, attach to intestine and body wall anterior to anus
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2–4 mm (0.08–0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex].
Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]
Middle part of an organ (as opposed to the cortex)[WP].
this class is used in a very general sense
A decussation of the diencephalon where the fibers of the optic nerve cross
The point at which fibers of the optic nerves cross.[AAO]
The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]
OBSOLETE. Original definition: The pharyngeal nerve (pterygopalatine nerve) is a small branch arising from the posterior part of the pterygopalatine ganglion. It passes through the pharyngeal canal with the pharyngeal branch of the maxillary artery, and is distributed to the mucous membrane of the nasal part of the pharynx, behind the auditory tube. [WP,unvetted].
The thoracic ganglia are paravertebral ganglia. The thoracic portion of the sympathetic trunk typically has 12 thoracic ganglia. Emerging from the ganglia are thoracic splancic nerves (the cardiopulmonary, the greater, lesser, and least splanchic nerves) that help provide sympathetic innervation to abdominal structures. Also, the ganglia of the thoracic sympathetic trunk have both white and gray rami communicantes. The white rami carry sympathetic fibers arising in the spinal cord into the sympathetic trunk. [WP,unvetted].
The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted].
Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP]
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
This class excludes compound eye corneal lenses.
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
obsolete joint connecting hardened body parts
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
The smallest morphological and functional unit of the ➞compound eye that consists of a usually limited and often constant number of rhabdomeric ➞photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
The paired, usually multiple jointed, sensory organs articulating on the procephalic region of the head capsule; its highly versatile sensory structures are capable to detect the various environmental stimuli. In the context of Drosophila refers to they are the most anterior segmented sensory appendage of the head.
this term should be ceded to the arthropod anatomy ontology
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad].
in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum
Single element that constitutes the postzonal area of the pectoral girdle.[AAO]
relationship loss: part_of postzonal element (AAO:0000938)[AAO]
Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]
It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life
in birds, either ratite (no keel or carina) or carinate (keel and carina present)
While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad].
Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]
Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]
proximal metapterygial mesomere of pectoral appendage
proximal metapterygial mesomere of pectoral fin
the serous membrane surrounding the lungs and lining the walls of the pleural cavity
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
In MA, is_a cavity lining. In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See http://purl.obolibrary.org/obo/uberon/tracker/86
The portion of the hindlimb that contains both the stylopod and zeugopod.
The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot
The major preaxial endochondral bone in the posterior zeugopod[Phenoscape].
One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]
A bony prominence near the extremity of the femur that normally serves as attachment points for hip and thigh muscles[MP,modified]
Process on the ventral surface of the shaft of the femur.[AAO]
there are two in human (greater and lesser trochanters) and three in many other mammalian species (greater, lesser and third)
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]
Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]
proximal metapterygial mesomere of pelvic appendage
proximal metapterygial mesomere of pelvic fin
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
A metapodium region that is part of a pes.
mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
A flight organ of the adult external thorax that is derived from a dorsal mesothoracic disc.
TODO - review. hymenoptera thorax = fusion of thorax and mesosoma/metasoma
In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery
The capitate stalk on both sides of the thorax having developed from the dorsal metathoracic wing-buds, it is freely movable and capable of vibration, representing the hind wing of Diptera; used for flight balance.
Brainstrem structure that has as its parts the pontine tegmentum and basal part of pons[FMA].
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination
Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
the gonad of a female organism which contains germ cells
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus
A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]
in birds divided into infundibulum, magnum, isthmus, uterus, and vagina
tubular parts of female reproductive system
An organ of the female reproductive tract in insects, some molluscs, oligochaeta worms and certain other invertebrates and vertebrates.[1] Its purpose is to receive and store sperm from the male, and can sometimes be the site of fertilization when the oocytes are ready.[2] Some species have multiple spermathecae, as seen in earthworms, where four pairs of spermathecae are present. One pair in 6,7,8 and 9 segments. They receive and store the spermatozoa of another earthworm during copulation.[3] They are lined with epithelium and are variable in shape; some are thin, heavily coiled tubes, others are vague outpocketings from the main reproductive tract. It is one of the many variations in sexual reproduction[WP]. an accordion-like tube that contains sperm and is the site of oocyte fertilization.
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
external genital organs of the female mammal[WP].
The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.
Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]
(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]
The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid.
The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted].
A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct
The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]
Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.
A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP].
TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO
tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part
The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA].
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
OBSOLETE: The mostly slit-like opening on the body surface through which air is taken into the respiratory system.
This class was obsoleted as it grouped together disparate classes. For the fish structure, see UBERON:0010019. The arthropod structure will presumably be added to the arthropod anatomy
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
The body of the ulna at its upper part is prismatic in form, and curved so as to be convex behind and lateralward; its central part is straight; its lower part is rounded, smooth, and bent a little lateralward. It tapers gradually from above downward, and has three borders and three surfaces.
Blood analogue used by all arthropods and most mollusks that have an open circulatory system. In these animals there is no distinction between blood and interstitial fluid. The liquid fills all of the interior (the hemocoel) of the body and surrounds all cells.
The head of the radius has a cylindrical form, and on its upper surface is a shallow cup or fovea for articulation with the capitulum (or capitellum) of the humerus. The circumference of the head is smooth; it is broad medially where it articulates with the radial notch of the ulna, narrow in the rest of its extent, which is embraced by the annular ligament. The deepest point in the fovea is not axi-symmetric with the long axis of the radius, creating a cam effect during pronation and supination[WP].
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
WP says this is the analog of peripheral nerves in CNS.
A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed).
note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'
Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A portion of tissue which is a fasiculated group of axons.[TAO]
The region of a neuron receiving inputs from other neurons, typically a slender neurite, often branched. In insect neurons, this is often not a clear designation and often presynaptic sites co-extend with postsynaptic ones.
Made obsolete as it was equivalent to GO class
One of the processes or extensions of a neuron, axon or dendrite or cell body fiber. // Cell appendage of the neuron which includes the axon and the dendrite.
The structural contact that is the site of transmission between neurons, identified by a presynaptic ribbon and synaptic vesicles as the input element and one or (usually) more postsynaptic elements with various specializations (membrane densities, cisternae, etc.).
General anatomical term applied to nerves in which somatic efferent nerve fibers predominate[FMA]. A motor nerve is an efferent nerve that exclusively contains the axons of somatic and branchial motoneurons, which innervate skeletal muscles (that ensure locomotion) and branchial muscles (that motorize the face and neck)[WP].
A group of neurons that provides a nervous response from a tissue[AEO].
General anatomical term applied to nerves in which somatic afferent nerve fibers predominate[FMA]. nerves that receive sensory stimuli made up of nerve fibers, called sensory fibers (mechanoreceptor fibers sense body movement and pressure placed against the body, and nociceptor fibers sense tissue injury)[WP][Wikipedia:Sensory_nerve].
A diaphysis that is part of a radius bone[Automatically generated definition].
The body of the radius (or shaft of radius) is prismoid in form, narrower above than below, and slightly curved, so as to be convex lateralward. It presents three borders and three surfaces[Wikipedia:Body_of_radius].
synapsis neuromuscularis; junctio neuromuscularis
thin membranous sheath around a nerve fiber[TFD].
FMA def is 'Neural tissue which consists of Schwann cells' which does not fit, but we still use 'neural tissue' here. WP def specifically states Schwann cells, which would restrict it to PNS
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
The sensory system for the sense of taste.
The sensory system for the sense of taste[NIFSTD:nlx_anat_090803].
The sensory system used for the sense of taste.[AAO]
in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
Can refer to a light sensitive organ, a photoreceptor cell or a photoreceptor protein. This class was made obsolete because it was ambiguous
Fibrous joint in which the periodontal ligament connects a tooth to the alveolar bone of the maxilla or mandible. Examples: Dento-alveolar joint of incisor tooth.[FMA]
A filament, mostly protein, that grows from follicles found in the dermis[WP].
TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)
Chordotonal organs are arthropod sensory structures consisting of special sensilla called the scolopidia, which are mechano-transducers and respond mainly to stretch or flexion. In insects, they consist of bundles of internal sensilla, each of which has a cap cell, an enveloping cell and one or more sense cells. The distal end of the organ is usually attached to the cuticle of the body wall, marked by a pit, a thickened disc or a nodule of chitin, and the base of the organ is connected with the hypodermis, often by a special ligament.
To be ceded to Arthropod anatomy ontology
A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells
In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN10:0073040584 (Vertebrates, Kardong)]
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
saliva-secreting exocrine glands of the oral cavity[GO]
currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.
A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]
The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
The caudalmost subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - UBERONREF:0000002). We may explicitly make this a developmental class
the caudal portion of the primitive digestive tube of the embryo
Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets[NIF].
isa or partof neuropil? TODO. Add to GO-CC?
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
Anatomical chamber. Examples: right atrium of heart, atrium of middle nasal meatus, atrium of tympanic cavity, atrium of alveolus.
obsoleted because 'atrium' as a general grouping class that encompasses the cardiac atrium and atrium of alveolus atrium is of questionable value. Furthermore, the use of the term 'atrium' in the generic sense is misleading, as this is commonly used to refer specifically to the cardiac atrium
Bottom part of the pharynx that connects to the esophagus.
The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG]
the terminal portion of the intestinal tube, terminating with the anus
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
A system of neurons that has the specialized function to produce and secrete hormones, and that constitutes, in whole or in part, an endocrine organ or system.
currently intended for invert structure; alt definitions include: organs in which intimate relationships between axons and terminal blood vessels are established
brain areas from which substances enter blood for example, the neurohypophysis from which oxytocin and vasopressin enter blood.
A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified].
this will be ceded to the Arthropod Anatomy Ontology
It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]
One of a pair of neurohemal organs located on the walls of the aorta just behind the brain. The corpora cardiaca release their store of PTTH only after they receive a signal from neurosecretory cells in the brain.
will be ceded to arthropod anatomy ontology
One of a pair of separate or fused bodies in many insects that are sometimes closely associated with the corpora cardiaca and that secrete hormones (as juvenile hormone)[BTO].
In Lepidoptera species, the corpus allatum acts as a release site for prothoracicotropic hormone which is generated by the brain
In many Diptera species, the corpus allatum is fused with the corpus cardiacum, forming Weismann's ring
Prominent lobed neuropils found in annelids and all arthropods except crustaceans. They are thought to be involved in olfactory associative learning and memory[MESH] Mushroom body neuropils are divided into calyces, pedunculus, and its subsequent lobes. In Drosophila these are the alpha, beta, and gamma lobes.
Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'
A neurosecretory center of the insect brain, located along the anterior midline[wiktionary]. A medial cleft or depression dividing the left and right protocerebrum and containing numerous large and small somata of neurosecretory and neuromodulatory neurons[FBbt].
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
the small lobe of the cerebellum at the posterior border of the middle cerebellar peduncle anterior to the biventer lobule that receives input from the inferior and medial vestibular nuclei and sends fibers back to the vestibular nuclei, and processes and integrates these signals to allow for the constant maintenance of balance
At its base, the flocculus receives input from the middle ears vestibular system and regulates balance. Many floccular projections descend to the spinal cord and connect to the motor nuclei involved in control of eye movement.
flocculus is an exact label for two distinct classes in NIF.
A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue
These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]
Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.
It passes through the buccal fat, buccopharyngeal fascia, and buccinator muscle then opens into the vestibule of the mouth opposite the upper second molar tooth. The buccinator acts as a valve that prevents inflation of the duct during blowing. Running along with the duct superiorly is the transverse facial artery and upper buccal nerve; running along with the duct inferiorly is the lower buccal nerve[Wikipedia:Parotid_duct]
A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core.
strictly speaking the term intervertebral disk [applies to intervertebral cartilage]
whose gel-like core is nucleus puloposus, by this definition only in mammals
A synovial joint between the prezygapophysis of one vertebra and the postzygapophysis of the vertebra directly above it. There are two facet joints in each spinal motion segment[WP].
A zone of skin that is part of a back [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
The head of pancreas is a portion of the pancreas that is lodged within the curve of the duodenum, and is flattened anteriorly (from before). The other parts of the pancreas are the body and the tail. Its upper border is overlapped by the superior part of the duodenum and its lower overlaps the horizontal part; its right and left borders overlap in front, and insinuate themselves behind, the descending and ascending parts of the duodenum respectively. [WP,unvetted].
Hagfish and lampreys may have one or more endocrine buds - and later the vertebrate pancreas develop as independent ventral and dorsal buds that eventually fuse to become one organ.[well established][VHOG]
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. .
superficial branch of transverse cervical artery
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice
Cavity of serous sac surrounded by serous pericardium.[FMA]
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
A vertebral centrum element that is composed primarily of a bone tissue.
Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO]
Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO]
The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra].
The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO]
VSAO definition states it surrounds notochord but not applicable to post-natal.
The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback.
Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]
Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]
Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]
relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]
The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted].
Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae.
the two short, thick processes, which project backward, one on either side, from the upper part of the body to the laminae
Paired processes at the cephalic end of the neural arch. The articular facets of the prezygapophyses face dorsomedially and articulate with the lateroventrally facing facets of the postzygapophyses of the preceding vertebra.
TODO - add distinct classes for hemal vs neural?
Paired, anteromedially directed processes from the neural arches, ligamentously joined to the postzygapophyses of the preceding vertebra.[TAO]
Paired processes at the caudal end of the neural arch. The articular facets of the postzygapophyses face lateroventrally and articulate with the dorsomedially facing facets of the prezygapophyses of the succeeding vertebra.
Paired, dorsomedially directed processes on the posterior ends of the centra, ligamentously joined to the neural prezygapophyses of the immediately posterior vertebra.[TAO]
Posteriorly projecting processes allowing de facto contact between consecutive vertebrae (some soft tissues are also present) via articular facets. [PHENOSCAPE:NI]
Endocardium that is part of the cardiac ventricle.
An epicardial layer that lines a cardiac ventricle
The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
A zone of skin that is part of a head [Automatically generated definition].
A zone of skin that is part of a trunk [Automatically generated definition].
obsoleted as it conflated two distinct classes
Transudate contained in the pleural cavity.[FMA]
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
Secretion produced by a sweat gland.[FMA]
Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.[FMA]
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar.
we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeous tooth. Note that sea cucumbers develop calcareous tooth-like structures
The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]
absent in living platypus, present in toothed Miocene platypus Obduron dicksoni
The first vertebral bone in the vertebral column.
First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]
Vertebra that is posteriorly adjacent to the neurocranium.[TAO]
The second vertebral bone in the vertebral column.
Vertebra that is posteriorly adjacent to vertebra 1.[TAO]
A vertebra bone that is part of the sacral region of the vertebral column.
todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs)
Enlarged vertebra with transverse processes (diapophyses), and ocassionally ribs, that are modified and elaborated for support of the pelvic girdle.[AAO]
Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx).
Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]
we deliberately merge the MA classes as we believe them equivalent
Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae
An anatomical wall that is part of a esophagus [Automatically generated definition].
the lymph nodes located around the axillary vein that receive lymphatic drainage from the upper or forelimb, scapular region and pectoral region
Incisors are the first kind of tooth in heterodont mammals. They are located in the premaxilla above and mandible below. [WP,unvetted].
Humans normally have eight (8) incisors; Among other animals, some other primates, cats and horses have twelve. Rodents have four, while Foxes have nine. Rabbits and hares (lagomorphs) were once considered rodents, but are distinguished by having eight — one small pair, called 'peg teeth', is located directly behind the most anterior pair. Incisors are used to bite off tough foods, such as red meat
The subcostal vein is a vein in the human body that runs along the bottom of the twelfth rib. It has the same essential qualities as the posterior intercostal veins, except that it cannot be considered intercostal because it is not between two ribs. Each subcostal vein gives off a posterior (dorsal) branch which has a similar distribution to the posterior ramus of an intercostal artery. [WP,unvetted].
The Pectoralis minor is a thin, triangular muscle, situated at the upper part of the chest, beneath the Pectoralis major. [WP,unvetted].
The external jugular vein receives the greater part of the blood from the exterior of the cranium and the deep parts of the face, being formed by the junction of the posterior division of the posterior facial with the posterior auricular vein. [WP,unvetted].
Vein which collects blood from the muscles of the head and tongue and the thyroid gland.[AAO]
A cartilage that is part of a main bronchus [Automatically generated definition].
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control
The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)
The anterior jugular vein begins near the hyoid bone by the confluence of several superficial veins from the submaxillary region. It descends between the median line and the anterior border of the Sternocleidomastoideus, and, at the lower part of the neck, passes beneath that muscle to open into the termination of the external jugular, or, in some instances, into the subclavian vein. It varies considerably in size, bearing usually an inverse proportion to the external jugular; most frequently there are two anterior jugulars, a right and left; but sometimes only one. Its tributaries are some laryngeal veins, and occasionally a small thyroid vein. Just above the sternum the two anterior jugular veins communicate by a transverse trunk, the venous jugular arch, which receive tributaries from the inferior thyroid veins; each also communicates with the internal jugular. There are no valves in this vein. [WP,unvetted].
A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad].
Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]
relationship loss: part_of zonal element (AAO:0000936)[AAO]
In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]
The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X].
In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.
FMA and MA differ in whether they consider this part of the shoulder
A superficial vein of the upper limb that communicates with the basilic vein via the median cubital vein at the elbow and is located in the superficial fascia along the anterolateral surface of the biceps brachii muscle. Superiorly the cephalic vein passes between the deltoid and pectoralis major muscles and through the deltopectoral triangle, where it empties into the axillary vein. It is often visible through the skin, and its location in the deltopectoral groove is fairly consistent, making this site a good candidate for cannulation. It is often referred to as the 'House-man's Friend' for this reason and is generally a good place for cannulaton when a large bore cannula needs to be sited. [WP,modified].
The sternohyoid muscle is a thin, narrow muscle attaching the hyoid bone to the sternum, one of the paired strap muscles of the infrahyoid muscles serving to depress the hyoid bone. It is innervated by the ansa cervicalis. The muscle arises from the posterior border of the medial end of the clavicle, the posterior sternoclavicular ligament, and the upper and posterior part of the manubrium sterni. Passing upward and medially, it is inserted by short tendinous fibers into the lower border of the body of the hyoid bone. [WP,unvetted].
The sternohyoid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical plexus; it attaches to the hyoid appratus and the sternum.[FEED]
Note that as defined here, this structure attaches to the sternum, which is a tetrapod structure. TAO has class 'sternohyoid' as part of mandibular muscle, but no sternum, so excluded here. The TAO/ZFA class has no definition, but the dictionary of icthyology states: 'a large muscle originating on the ventral spine of the postcleithrum and inserting on the sides of the urohyal. It functions in rapid opening of the jaw and expanding the buccal cavity' - a generic way of grouping these is via a hyoid - girdle connection
The omohyoid muscle is a muscle at the front of the neck that consists of two bellies separated by an intermediate tendon. It belongs to the group of infrahyoid muscles. [WP,unvetted].
The omohyoid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical plexus; it attaches to the hyoid appratus and the scapula.[FEED]
The Sternothyreoideus (or Sternothyroid muscle) is shorter and wider than the Sternohyoideus, beneath which it is situated. It arises from the posterior surface of the manubrium sterni, below the origin of the Sternohyoideus, and from the edge of the cartilage of the first rib, and sometimes that of the second rib, it is inserted into the oblique line on the lamina of the thyroid cartilage. This muscle is in close contact with its fellow at the lower part of the neck, but diverges somewhat as it ascends; it is occasionally traversed by a transverse or oblique tendinous inscription. [WP,unvetted].
The sternothyroid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical plexus; it attaches to the thyroid cartilage and the sternum.[FEED]
The thyrohyoid muscle is a small, quadrilateral muscle appearing like an upward continuation of the Sternothyreoideus. It belongs to the infrahyoid muscles group. It arises from the oblique line on the lamina of the thyroid cartilage, and is inserted into the lower border of the greater cornu of the hyoid bone. [WP,unvetted].
The thyrohyoid is a somitic muscle that participates in oral/pharyngeal behaviors and is innervated by C1 and Cranial Nerve XII ; it attaches to the thyroid cartilage and the hyoid apparatus.[FEED]
the respiratory muscles that arise from the lower border of one rib and insert into the upper border of the adjoining rib
Inspiration by active expansion of the thorax evolved later, in the ancestor of reptiles, birds, and mammals. This was powered originally by the intercostal muscles (as in lizards or crocodilians) and later (in mammals only) by a muscular diaphragm.[well established][VHOG]
The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted].
Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe.
some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts
The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]
The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].
Portion of the liver which develops on the fish's left side.[TAO]
The quadrate lobe is an area of the liver situated on the under surface of the right lobe, bounded in front by the anterior margin of the liver; behind by the porta hepatis; on the right, by the fossa for the gall-bladder; and on the left, by the fossa for the umbilical vein. It is oblong in shape, its antero-posterior diameter being greater than its transverse. [WP,unvetted].
The portion of the right lobe of the liver between the gall bladder, the porta hepatis, the round ligament and the lower margin of the organ. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The caudate lobe (posterior hepatic segment I, Spigelian lobe) is situated upon the postero-superior surface of the liver on the right lobe of the liver, opposite the tenth and eleventh thoracic vertebrae. It is bounded on the left side by the physiological division of the liver called the ligamentum venosum. It is bounded, below, by the porta; on the right, by the fossa for the inferior vena cava; and, on the left, by the fossa for the ductus venosus. It looks backward, being nearly vertical in position; it is longer from above downward than from side to side, and is somewhat concave in the transverse direction. The caudate process is a small elevation of the hepatic substance extending obliquely and laterally, from the lower extremity of the caudate lobe to the under surface of the right lobe. It is situated behind the porta, and separates the fossa for the gall-bladder from the commencement of the fossa for the inferior vena cava. Budd-Chiari syndrome, caused by occlusion of hepatic venous outflow, can lead to hypertrophy of the caudate lobe due to its own caval anastomosis that allows for continued function of this lobe of the liver. [WP,unvetted].
The portion of the right lobe of the liver between the fissure of the ligamentum venosum and the bare area of the liver. It ends into the superior recess of the lesser peritoneal sac. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The caudate lobe is the only real and constant hepatic lobe of mammals (...) .[well established][VHOG]
A lobe of tissue that is part of a thyroid gland.
Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids
A lobe of thyroid gland that is in the right side of a thyroid gland.
A lobe of thyroid gland that is in the left side of a thyroid gland.
The Longus colli muscle is a muscle of the human body. The Longus colli is situated on the anterior surface of the vertebral column, between the atlas and the third thoracic vertebra. It is broad in the middle, narrow and pointed at either end, and consists of three portions, a superior oblique, an inferior oblique, and a vertical. The superior oblique portion arises from the anterior tubercles of the transverse processes of the third, fourth, and fifth cervical vertebræ and, ascending obliquely with a medial inclination, is inserted by a narrow tendon into the tubercle on the anterior arch of the atlas. The inferior oblique portion, the smallest part of the muscle, arises from the front of the bodies of the first two or three thoracic vertebræ; and, ascending obliquely in a lateral direction, is inserted into the anterior tubercles of the transverse processes of the fifth and sixth cervical vertebræ. The vertical portion arises, below, from the front of the bodies of the upper three thoracic and lower three cervical vertebræ, and is inserted into the front of the bodies of the second, third, and fourth cervical vertebræ. [WP,unvetted].
The Scalenus medius, the largest and longest of the three scalene muscles, arises from the posterior tubercles of the transverse processes of the lower six cervical vertebræ. It descendes along the side of the vertebral column to insert by a broad attachment into the upper surface of the first rib, between the tubercle and the subclavian groove. The brachial plexus and the subclavian artery pass anterior to it. Because it elevates the upper ribs, the middle scalene muscle is also one of the accessory muscles of respiration. [WP,unvetted].
The Scalenus posterior (Scalenus posticus), the smallest and most deeply seated of the three Scaleni, arises, by two or three separate tendons, from the posterior tubercles of the transverse processes of the lower two or three cervical vertebræ, and is inserted by a thin tendon into the outer surface of the second rib, behind the attachment of the serratus ventralis. It is occasionally blended with the Scalenus medius. [WP,unvetted].
The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted].
The serratus dorsalis superior is a thin, quadrilateral muscle, situated at the upper and back part of the thorax. It arises by a thin and broad aponeurosis from the lower part of the ligamentum nuchae, from the spinous processes of the seventh cervical and upper two or three thoracic vertebræ and from the supraspinal ligament. Inclining downward and lateralward it becomes muscular, and is inserted, by four fleshy digitations, into the upper borders of the second, third, fourth, and fifth ribs, a little beyond their angles. [WP,unvetted].
A muscle that originates from the vertebrae and inserts in the ribs.
A paired muscle in the superficial layers of the anterior portion of the neck. It acts to flex and rotate the head. It also acts as an accessory muscle of inspiration, along with the scalene muscles of the neck. [WP,unvetted].
TODO: sternocleidomastoid = sternomastoid + Cleidomastoideus. Origin: from manubrium sterni (sterno) and clavicle (cleido) and it's insertion at the mastoid process of the temporal bone.
The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG]
The subscapularis is a large triangular muscle which fills the subscapular fossa and inserts into the lesser tubercle of the humerus and the front of the capsule of the shoulder-joint. [WP,unvetted].
Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton
Anatomical cluster that consists of all the vertebra in the body.[VSAO]
The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]
Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]
In a typical vertebra, the vertebral foramen is the foramen formed by the anterior segment, and the posterior part, the vertebral arch. The vertebral foramen begins at cervical vertebrae #1 and continues inferior to lumbar vertebrae #5. Within this foramen the spinal cord and associated meninges are housed. [WP,unvetted].
Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO]
The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism.
Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]
Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]
The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]
Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]
In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch
table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity.
Muscle composed of cardiac muscle cells that is part of the heart[ZFA]. involuntary striated muscle found in the walls of the heart, specifically the myocardium[Wikipedia]. Tissue which consists of cardiac myocytes surrounded by cardiac endomysium. Examples: Cardiac muscle tissue proper, conducting tissue of heart[FMA].
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. Tissue which consists of smooth muscle . Examples: Arrector muscle of hair, Muscularis mucosae.
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
The dorsal part of an animal, which in vertebrares includes the vertebral column. [cjm].
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
A vein that drains the pelvis and lower limbs into the inferior vena cava.
In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries.
Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.
The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].
in EHDAA2, the renal vein is part of the kidney
A renal vein that drains the right kidney
A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus].
A renal vein that drains the left kidney
A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus].
Vein that carries blood away from the liver[ZFA].
todo - add developmental relationships for other taxa
A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis.
TODO - check testicular vs spermatic vein (MA:0002218)
In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel
The ovarian vein, the female gonadal vein, carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. It is the female equivalent of the testicular vein, and is the venous counterpart of the ovarian artery. It can be found in the suspensory ligament of the ovary. It a paired vein, with one supplying each ovary. The right ovarian vein travels through the suspensatory ligament of the ovary and generally joins the inferior vena cava. The left ovarian vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. [WP,unvetted].
gonad of female reproductive system vein
gonada of female reproductive system vein
vein of female reproductive system gonad
vein of female reproductive system gonada
vein of gonad of female reproductive system
vein of gonada of female reproductive system
The Suprarenal veins are two in number: the right ends in the inferior vena cava. the left ends in the left renal or left inferior phrenic vein. They receive blood from the adrenal glands and will sometimes form anastomoses with the inferior phrenic veins. [WP,unvetted].
The median nerve is a nerve in humans and other animals. It is in the upper limb. It is one of the five main nerves originating from the brachial plexus. The median nerve is formed from parts of the medial and lateral cords of the brachial plexus, and continues down the arm to enter the forearm with the brachial artery. It originates from the brachial plexus with roots from C5, C6, C7, C8 & T1. The median nerve is the only nerve that passes through the carpal tunnel, where it may be compressed to cause carpal tunnel syndrome. [WP,unvetted].
A large triangular surface of the liver devoid of peritoneal covering.
The body of the pancreas is a subsection of the pancreas organ in the human body. It is somewhat prismatic in shape, and has three surfaces: anterior, posterior, and inferior. It is at the same level as the transpyloric plane. [WP,unvetted].
The tail of the pancreas, located anatomically left near the hilum of the spleen, is not simply an anatomical distinction. The tail is the only part of the pancreas which contains Pancreatic Polypeptide (PP) cells, which are responsible for secreting pancreatic polypeptide to coordinate exocrine and islet enzyme release. PP cells are found in the tail's periphery. Beta cells and delta cells are found in the central part of the tail as with the rest of the pancreas. The cells described above are located exclusively in the islet cells; their secretions reach exocrine portions of the pancreas via the capillary network surrounding the islet cell populations. [WP,unvetted].
the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct
Duct that connects the gall bladder and the common bile duct.[TAO]
The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
Kardong: in some herbivorous lizards, a cecum is present between small and large intestines
A blind-ended tube connected to the cecum, from which it develops embryologically[WP].
Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542].
A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG]
Last portion of the large intestine before it becomes the rectum.
TODO - abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
Segment of the colon which is continuous with the cecum proximally and the transverse colon distally.[FMA,modified]
The segment of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon.
The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong].
The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
we include this as zone of stomach even though it is not distinguished by gland type
The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]
We follow Kardong in defining stomach regions by glands.
Boundary notes: There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that "The gastric cardia is now clearly considered to be part of the stomach"[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]
The lesser curvature of the stomach, extending between the cardiac and pyloric orifices, forms the right or posterior border of the stomach. It descends as a continuation of the right margin of the esophagus in front of the fibers of the right crus of the diaphragm, and then, turning to the right, it crosses the first lumbar vertebra and ends at the pylorus. Nearer its pyloric than its cardiac end is a well-marked notch, the incisura angularis, which varies somewhat in position with the state of distension of the viscus; it serves to separate the stomach into a right and a left portion. The lesser curvature gives attachment to the two layers of the hepatogastric ligament, and between these two layers are the left gastric artery and the right gastric branch of the hepatic artery. [WP,unvetted].
The greater curvature of the stomach is directed mainly forward, and is four or five times as long as the lesser curvature. [WP,unvetted].
the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells
the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum
The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between
An anatomical wall that is part of a small intestine [Automatically generated definition].
An anatomical wall that is part of a large intestine [Automatically generated definition].
The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP].
The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids.
Hollow tree organ, the organ parts of which consists of the bile ducts[FMA].
Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct
Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]
The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP].
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part
The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct.
The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]
The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct.
The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]
The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space.
Anatomical cavity bounded by visceral and parietal peritoneum
The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
classified as a cavity in EHDAA2, organ segment in FMA. We hedge and use a union
A large vessel supplying the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra.
Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon
In human anatomy, the inferior mesenteric artery, often abbreviated as IMA, supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted].
One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates.
renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.
Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]
The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]
Renal artery that supplies the right kidney
The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP]
Renal artery that supplies the left kidney
The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP]
One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad.
A testicular artery that supplies a right testicle.
A testicular artery that supplies a left testicle.
In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP].
The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted].
In human anatomy, the left gastric artery arises from the celiac artery, and runs along the superior portion of the lesser curvature of the stomach. Branches also supply the lower esophagus. The left gastric artery anastomoses with the right gastric artery, which supplies the inferior portion. [WP,unvetted].
Artery that supplies blood to the liver.[TAO]
In anatomy, the splenic artery (in the past called the lienal artery) is the blood vessel that supplies oxygenated blood to the spleen. It branches from the celiac artery, and follows a course superior to the pancreas. [WP,unvetted].
The inferior pancreaticoduodenal artery is a branch of the superior mesenteric artery or from its first intestinal branch, opposite the upper border of the inferior part of the duodenum. It courses to the right between the head of the pancreas and duodenum, and then ascends to anastomose with the anterior and posterior superior pancreaticoduodenal artery. It distributes branches to the head of the pancreas and to the descending and inferior parts of the duodenum. [WP,unvetted].
arteriae pancreaticoduodenales inferiores
The middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers’ breadth from the transverse colon, to which they distribute branches. [WP,unvetted].
The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted].
Each (left and right) superior suprarenal artery is a branch of the inferior phrenic artery on that side of the body. The left and right phrenic arteries supply the diaphragm, and come off the aorta. [WP,unvetted].
superior adrenal branch of inferior phrenic artery
superior suprarenal branch of inferior phrenic artery
The mucosal layer that lines the stomach.
The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa].
the fibrous connective tissue layer beneath the stomach mucosa
the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum
anatomical wall of stomach serous membrane
anatomical wall of ventriculus serous membrane
serosa of anatomical wall of ventriculus
serous membrane of anatomical wall of stomach
serous membrane of anatomical wall of ventriculus
serous membrane of stomach anatomical wall
serous membrane of ventriculus anatomical wall
ventriculus anatomical wall serous membrane
A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP].
(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]
the thin layer of smooth muscle in the mucosal layer of the stomach that functions to agitate the surface area stomach mucosa by moving the villi back and forth
agitate the surface area stomach mucosa by moving the villi back and forth
lamina muscularis mucosae (tunica mucosa)(gaster)
A mucosa that is part of a small intestine [Automatically generated definition].
submucosal tissue in the small intestines.
A serous membrane that is part of a small intestine [Automatically generated definition].
duodenum, 1st part serosa, 2nd - 4th adventitia
A mucosa that is part of a large intestine [Automatically generated definition].
A submucosa that is part of a large intestine [Automatically generated definition].
A serous membrane that is part of a large intestine [Automatically generated definition].
A muscularis mucosa that is part of a small intestine.
lamina muscularis mucosae (tunica mucosa)(intestinum tenue)
lamina muscularis of small intestine mucous membrane
the protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles
Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas).
FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]
Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs
aggregated lymphoid follicle of intestine
A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP].
currently defined as equivalent to any submucosal gland in the duodenum.
Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds
the tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold
in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all speciesi for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]
the BTO class refers to a generic villous
The pancreatic veins consist of several small vessels which drain the body and tail of the pancreas, and open into the trunk of the great pancreatic vein. [WP,unvetted].
see also MA:0002165 ! lieno-pancreatic vein
A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
The jejunal veins are tributaries of the superior mesenteric vein. [WP,unvetted].
The veins that drain blood from the ileum into the superior mesenteric vein.
The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted].
The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted].
The Quadratus lumborum is irregular and quadrilateral in shape, and broader below than above. [WP,unvetted].
The transversus abdominis muscle, also known as the transversalis muscle and transverse abdominal muscle, is a muscle layer of the anterior and lateral abdominal wall which is just deep to (layered below) the internal oblique muscle. It is thought to be a major muscle of the functional core of the human body; although some argue that due to its small cross-sectional area, it cannot generate the forces required to be a prime core stabilizer. [WP,unvetted].
One of a pair of transverse abdominal muscles that is the anterolateral muscle of the abdomen, lying immediately under the internal abdominal oblique. [TFD][VHOG]
Behind the thorax, the lateral group (of muscles in reptiles and mammals) remains essentially as for amphibians. (It breaks into three sheet-like layers: external oblique muscle, the internal oblique, and the transversus). More anteriorly, however, the ribs, now enlarged, penetrate and alter this group of muscles. The transversus is excluded from the thorax and the external and internal obliques become, respectively, the external and internal intercostal muscles, which contribute to the new function of ventilation of the lungs.[well established][VHOG]
An ureter that is part of a right side of organism [Automatically generated definition].
An ureter that is part of a left side of organism [Automatically generated definition].
A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP].
In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter
Region of parenchyma of kidney representing the outer portion.[FMA]
portion of the urinary collecting system within the kidney that drains several minor calyces
major calyx collects urine from several renal papillae; all major calyces unite to form the renal pelvis
portion of the urinary collecting system within the kidney that drains one renal papilla
one renal papilla projects into the lumen of one minor calyx; several minor calyces unite to form a major calyx
Tip of renal pyramid projecting into a minor calyx.
the structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron
A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]
A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]
The part of the nephron that filters blood.[TAO]
Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron
A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus
Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]
Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP].
One fold of the S-shaped body gives rise to Bowman’s capsule[GUDMAP]
An epithelial tube that is part of the nephron, the functional part of the kidney.
note that in ISBN10:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA
The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient
Renal duct that collects the output from renal tubules.[TAO]
in ISBN10:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron
An adrenal gland that is in the right side of the abdomen
In humans, the right adrenal gland is triangular shaped
An adrenal gland that is in the left side of the abdomen
In humans, the left adrenal gland is semilunar shaped
the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO
the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine
Lamina propria that is part_of the small intestine.
lamina propria mucosa of small intestine
lamina propria mucosae of small intestine
lamina propria of mucosa of small intestine
A muscularis mucosa that is part of a large intestine.
lamina muscularis of large intestine mucosa
lamina muscularis of large intestine mucous membrane
A muscularis mucosa that is part of a intestine.
the tubular intestinal glands found in the mucosal membranes of the small intestine
The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)
A serous membrane that is part of a wall of intestine [Automatically generated definition].
anatomical wall of bowel serous membrane
anatomical wall of intestine serous membrane
intestine anatomical wall serous membrane
serous membrane of anatomical wall of bowel
serous membrane of anatomical wall of intestine
serous membrane of bowel anatomical wall
serous membrane of intestine anatomical wall
the smooth muscle ring, formed by an increase of the circular muscle fibers of the rectum, situated at the upper end of the anal canal, internal to the outer voluntary external anal sphincter
circular layer of anal muscularis externa
circular layer of muscularis externa of anal canal
circular layer of muscularis propria of anal canal
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
opening of terminal part of digestive tract
The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad.
A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP].
in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament
The splenic hilum is a location on the surface of the spleen. It is the point of attachment for the gastrosplenic ligament, and the point of insertion for the splenic artery and splenic vein. [WP,unvetted].
The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur
the parenchymatous tissue network of the spleen that consists of loose plates or cords (sinuses) infiltrated with red blood cells where most of the blood filtration occurs and degenerate erythrocytes are removed from the circulation
the zone between the red and white pulp of the spleen containing numerous macrophages and lymphocytes, and a rich plexus of sinusoids supplied by white pulp arterioles carrying blood-borne antigens
WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line.
A lamina propria that is part of a ureter [Automatically generated definition].
The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP]
MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
An anatomical wall that is part of a urinary bladder [Automatically generated definition].
the smooth triangular region of the wall of the urinary bladder formed by the two ureteral orifices and the internal urethral orifice; it is an area in which the muscle fibers are closely adherent to the mucosa
The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill.
Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present
The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP].
the mucous membrane lining the urinary bladder
A serous membrane that is part of a urinary bladder [Automatically generated definition].
A lamina propria that is part of a urinary bladder [Automatically generated definition].
lamina propria mucosa of urinary bladder
lamina propria mucosae of urinary bladder
An anatomical wall that is part of a intestine [Automatically generated definition].
we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different
The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct.
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
A structure found in the red pulp of the spleen between the sinusoids, consisting of fibrils and connective tissue cells with a large population of monocytes and macrophages. These cords contain half of the human body's monocytes as a reserve so that after tissue injury these monocytes can move in and aid locally sourced monocytes in wound healing. Erythrocytes pass through the cords of Billroth before entering the sinusoids. The passage into the sinusoids may be seen as a bottleneck, where erythrocytes need to be flexible in order to pass through. In disorders of erythrocyte shape and/or flexibility, such as hereditary spherocytosis, erythrocytes fail to pass through and get phagocytosed, causing extravascular hemolysis.
The femoral nerve, the largest branch of the lumbar plexus, arises from the ventral divisions of the second, third, and fourth lumbar nerves. It descends through the fibers of the Psoas major, emerging from the muscle at the lower part of its lateral border, and passes down between it and the Iliacus, behind the iliac fascia; it then runs beneath the inguinal ligament, into the thigh, and splits into an anterior and a posterior division. Under the inguinal ligament, it is separated from the femoral artery by a portion of the Psoas major. [WP,unvetted].
Transudate contained in the peritoneal cavity.[FMA]
The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted].
Cavity for the articulation of the proximal bone of the hind limb.[AAO]
During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG]
In reptiles and in birds, the acetabula are deep sockets.
whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface.
A ring of bone formed by the sacrum and the first few coccygeal vertebrae as the roof, the pubis and ischia as the floor and the ilia and the acetabular part of the ischia as the walls.
TODO add taxon-specific part of relations connecting sub-structures to this.
in FMA, this is part of the axial skeletal system
Subdivision of lower limb or fin which links the paired limb/fin to the body[FMA,modified]. Examples: There are only two instances, right and left pelvic girdle regions.
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
A fused bone consisting of the ilium, ischium and and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified].
currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage
The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column
in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra.
Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad].
Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO]
All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium
Endochondral bone that is paired, forming the posterior part of the pelvis, articulating with the pubis and ilium.
Paired bones of endochondral origin that constitute the posterior elements of the pelvic girdle. They are synostotically fused to each other and form the posterior part of the acetabulum.[AAO]
this is_a hip bone in MA; in FMA it is a zone of bone organ.
A paired endochondral bone making up the anteroventral region of the tripartite pelvic girdle forming part of the ventral edge of the acetabulum. The origin site of many proximal hindlimb muscles. [PHENOSCAPE:ad].
Paired, cartilaginous (ocassionally calcified) elements that form the ventral portion of the pelvic girdle. Each is located ventral to the acetabulum between the anteroventral margin of the ischium and the posteroventral margin of the illium. When the element calcifies or ossifies, its articulation with adjacent elements is difficult to distinguish. Both pubes are synchondrotically fused to one another.[AAO]
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]
An epithelium that is part of a large intestine [Automatically generated definition].
the three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel
The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver.
The functional units of the liver including the lobules.
the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]
Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers.
(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]
the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule
Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct)
Fine tubular canals running between liver cells, throughout the parenchyma, usually occurring singly between each adjacent pair of cells, and forming a three-dimensional network of polyhedral meshes, with a single cell in each mesh[BTO]. A thin tube that collects bile secreted by hepatocytes. The bile canaliculi merge and form bile ductules, which eventually become common hepatic duct. Hepatocytes are polyhedral in shape, therefore having no set shape or design. They have surfaces facing the sinusoids, (called sinusoidal faces) and surfaces which contact other hepatocytes, (called lateral faces). Bile canaliculi are formed by grooves on some of the lateral faces of these hepatocytes. Microvilli are present in the canaliculi but are sparse. [WP,unvetted].
A column of tissue that is histologically identical to tissue found in the renal cortex, but which is located in the medulla between the renal pyramids.
Check part_of location against textual definition
The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]
kidney terms require review for cross-vertebrate compatibility and developmental relationships.
Functional unit of the kidney that filters waste.[TAO]
In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)
A narrow chalice-shaped cavity between the glomerular and capsular epithelium of the glomerular capsule of the kidney[TFD]. Between the visceral and parietal layers, into which the filtrate enters after passing through the podocytes' filtration slits[WP]. luminal region between the glomerular capsule visceral and parietal layers, into which filtrate enters after passing through the filtration barrier from the glomerular capillaries[MP]
Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO]
The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule.
Renal tubule that connects to the renal corpuscle.[TAO]
the section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine
the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review.
A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]
The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva .
The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids.
the portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure
The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule.
TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)
Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]
thick descending limb of proximal tubule
the distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule
TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions
loop of Henle ascending limb thick segment
straight portion of distal convoluted renal tubule
straight portion of distal convoluted tubule
The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa.
a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule].
in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter.
The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO].
Innermost region of the mammalian kidney.
the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy
The mucous membrane lining the uterus. [TFD][VHOG]
The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]
Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead
in FMA this is subdivided into basal and outer
the smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium
The muscular wall of the uterus. [TFD][VHOG]
In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG]
The myometrium stretches (the smooth muscle cells expand in both size and number) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss.
TODO - check for parallel structure with peritoneum
The psoas major is a long fusiform muscle placed on the side of the lumbar region of the vertebral column and brim of the lesser pelvis. It joins the iliacus muscle to form the iliopsoas. In less than 50 per cent of subjects the psoas major is accompanied by the psoas minor. [WP,unvetted].
the conic expansion of the corpus spongiosum that forms the head of the penis
the external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus.
In elephants the testes remain in the abdomen
In hedgehogs the testes remain in the inguinal canal
In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty
In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens
In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field
The scrotum of marsupials is not homologous with the scrotum of mammals[ISBN:113945742X]
the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens
A similar, but probably non-homologous, structure is found in cartilaginous fishes
Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
A fallopian tube that is part of a right side of organism [Automatically generated definition].
non-functional in monotremes[ISBN-13:978-0226870137]
A fallopian tube that is part of a left side of organism [Automatically generated definition].
layer of simple cuboidal cells covering surface of ovary[WP].
Controversial - see article. Requires expert input. Also check BTO placement
A spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified].
TODO - align subtypes based on staging, which is taxon-specific
Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO]
These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans)
follicle of ovary viewed macroscopically
At one part of the mature follicle, the cells of the membrana granulosa are collected into a mass which projects into the cavity of the follicle. This cluster of cells is termed the cumulus oophorus (Latin cumulus=heap, Greek oo=egg + phorus=carrying) discus proligerus, and it is released with the embedded oocyte during ovulation. In order for fertilization to occur this layer must be penetrated by the spermatocyte. [WP,unvetted].
A capsule that surrounds a female gonad.
The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted].
The internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted].
The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted].
todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships
The inferior vesical artery is an artery in the pelvis that supplies the lower part of the bladder. [WP,unvetted].
The superior vesical artery supplies numerous branches to the upper part of the bladder. From one of these a slender vessel, the artery to the ductus deferens, takes origin and accompanies the duct in its course to the testis, where it anastomoses with the internal spermatic artery. Other branches supply the ureter. The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery. [WP,unvetted].
The iliolumbar artery is a branch of the posterior trunk of the internal iliac artery. [WP,unvetted].
The obturator artery passes antero-inferiorly (forwards and downwards) on the lateral wall of the pelvis, to the upper part of the obturator foramen, and, escaping from the pelvic cavity through the obturator canal, it divides into both an anterior and a posterior branch. [WP,unvetted].
The superior gluteal artery (gluteal artery) is the largest branch of the internal iliac artery, and appears to be the continuation of the posterior division of that vessel. It is a short artery which runs backward between the lumbosacral trunk and the first sacral nerve, and, passing out of the pelvis above the upper border of the Piriformis, immediately divides into a superficial and a deep branch. Within the pelvis it gives off a few branches to the Iliacus, Piriformis, and Obturator internus, and just previous to quitting that cavity, a nutrient artery which enters the ilium. [WP,unvetted].
A large vein that connects the femoral vein to the common iliac vein. Their origin is at the inferior margin of the inguinal ligaments and they terminate when they join the internal iliac veins (to form the common iliac veins). Both external iliac veins are accompanied along their course by external iliac arteries. [WP,modified].
A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted].
The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted].
The iliolumbar vein is the vena comitans of the iliolumbar artery. The obturator nerve crosses superficial to it. A single vein is found more commonly than a double vein. It drains vertebral segments four and five. It is closely related to the ascending lumbar vein. [WP,unvetted].
The obturator vein begins in the upper portion of the adductor region of the thigh and enters the pelvis through the upper part of the obturator foramen, in the obturator canal. It runs backward and upward on the lateral wall of the pelvis below the obturator artery, and then passes between the ureter and the hypogastric artery, to end in the hypogastric vein. It has an anterior and posterior branch (similar to obturator artery). [WP,unvetted].
The sciatic nerve (also known as the ischiatic nerve) is a large nerve in humans and other animals. It begins in the lower back and runs through the buttock and down the lower limb. It is the longest and widest single nerve in the human body. The sciatic supplies nearly the whole of the skin of the leg, the muscles of the back of the thigh, and those of the leg and foot. In humans, it is derived from spinal nerves L4 through S3. It contains fibres from both the anterior and posterior divisions of the lumbosacral plexus. [WP,edited].
mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/
The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
A nerve arising at the terminal division of the sciatic nerve at the popliteal fossa and extending to the neck of the fibula, ultimately innervating the Peroneus muscle[MP]. The common peroneal nerve (common fibular nerve; external popliteal nerve; peroneal nerve), about one-half the size of the tibial nerve, is derived from the dorsal branches of the fourth and fifth lumbar and the first and second sacral nerves. It descends obliquely along the lateral side of the popliteal fossa to the head of the fibula, close to the medial margin of the biceps femoris muscle. It lies between the tendon of the biceps femoris and lateral head of the gastrocnemius muscle, winds around the neck of the fibula, between the peronæus longus and the bone, and divides beneath the muscle into the superficial peroneal nerve (superficial fibular nerve) and deep peroneal nerve (deep fibular nerve). [WP,unvetted].
Muscle (organ) which is a part of the pelvis. Examples: levator ani,
The Levator ani is a broad, thin muscle, situated on the side of the pelvis. It is attached to the inner surface of the side of the lesser pelvis, and unites with its fellow of the opposite side to form the greater part of the floor of the pelvic cavity. It supports the viscera in pelvic cavity, and surrounds the various structures which pass through it. In combination with the Coccygeus muscle, it forms the pelvic diaphragm. [WP,unvetted].
the levator ani muscle acts to lower the tail, in animals that have one
The Coccygeus is a muscle of the pelvic wall (i.e. peripheral to the pelvic floor), situated behind the levator ani and in front of the sacrospinous ligament. It is a triangular plane of muscular and tendinous fibers, arising by its apex from the spine of the ischium and sacrospinous ligament, and inserted by its base into the margin of the coccyx and into the side of the lowest piece of the sacrum. It assists the Levator ani and Piriformis in closing in the back part of the outlet of the pelvis. [WP,unvetted].
A portion of a prostate that forms a lobe.
Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder—namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue
The prostate lobe that appears as a thin tubular structure, attached to the lesser curvature of the paired seminal vesicles.
TODO - check - see comments from http://www.ncbi.nlm.nih.gov/pubmed/15163300
The pampiniform plexus is a network of many small veins found in the human male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted].
venous plexus of fascia of prostate gland
A zone of skin that is part of a penis [Automatically generated definition].
In male human anatomy, the foreskin is a retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. It is also described as the prepuce, a technically broader term that also includes the clitoral hood in women, to which the foreskin is embryonically homologous. [WP,unvetted].
A urethra that is part of a male reproductive system.
A urethra that is part of a female reproductive system.
the widest and most dilatable part of the male urethra canal which runs almost vertically through the prostate from its base to its apex, lying nearer its anterior than its posterior surface; this portion of the urethral canal is spindle-shaped, being wider in the middle than at either extremity, and narrowest below, where it joins the membranous portion; it is lined by transitional epithelium and contains in its posterior wall, or floor, the orifices of the prostatic utricle, ejaculatory ducts, and prostatic ducts, collectively known as the seminal colliculus (aka verumontanum)
the longest part of the male urethra contained in the corpus spongiosum and extending from the end of the membranous portion to the external urethral orifice; commencing below the inferior fascia of the urogenital diaphragm it passes forward and upward to the front of the symphysis pubis; and then, in the flaccid condition of the penis, it bends downward and forward; while narrow and of uniform size in the body of the penis, it is dilated behind, within the bulb, and again anteriorly within the glans penis, where it forms the fossa navicularis urethrae; the spongy urethra is lined by pseudostratified columnar epithelium proximally, and by stratified squamous epithelium distally
Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine
The ischiocavernosus muscle is a muscle just below the surface of the perineum, present in both men and women. [WP,unvetted].
The Dorsal Artery of the Penis ascends between the crus penis and the pubic symphysis, and, piercing the inferior fascia of the urogenital diaphragm, passes between the two layers of the suspensory ligament of the penis, and runs forward on the dorsum of the penis to the glans, where it divides into two branches, which supply the glans and prepuce. On the penis, it lies between the dorsal nerve and deep dorsal vein, the former being on its lateral side. It supplies the integument and fibrous sheath of the corpus cavernosum penis, sending branches through the sheath to anastomose with the deep artery of the penis. [WP,unvetted].
The lesser sac, also known as the omental bursa, is the cavity in the abdomen that is formed by the lesser and greater omentum. Usually found in mammals, it is connected with the greater sac via the epiploic foramen (also known as the Foramen of Winslow). In mammals, it is not uncommon for the lesser sac to contain considerable amounts of fat. In human anatomy, the wall of the stomach, pancreas and splenic artery are a part of the wall of the lesser sac. If these structures rupture they may leak into the lesser sac. For the stomach, which lies anterior to the omental bursa, the rupture must be on the posterior side; if it were anteriorly located, the leak would collect in the greater sac. The lesser sac is embryologically formed from an infolding of the greater omentum. The open end of the infolding, known as the epiploic foramen, is usually proximal to the stomach. [WP,unvetted].
The lesser sac of the peritoneum. Part of the peritoneal cavity behind the liver, lesser omentum and stomach. It lies across the transverse mesocolon and extends into the greater omentum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
classified as a cavity in EHDAA2, so this truly corresponds to FMA 'Cavity of lesser sac' - we hedge for now; todo - treat same as greater sac
The mesentery that suspends the ovary from the dorsal wall of the coelom[VHOG].
Anatomical structure consisting of a membrane which suspends the ovaries from the mesial side of the kidney.[AAO]
The mesentery that suspends the ovary from the dorsal wall of the coelom. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.560, see_Kardong_KV][VHOG]
the tubules in the testes where spermatogenesis occurs
Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]
One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]
Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG]
FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)
A membrane that surrounds or partially covers the vaginal opening.
Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified]
Adipose tissue, cells of which contain a single large lipid droplet.
A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified]
Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]
Anatomical cavity that connects an organ cavity, organ cavity subdivision or cavity of body part subdivision to the exterior, completely or partially surrounded by organs or organ parts that are lined by epithelium. Examples: preputial cavity, vestibule of vagina.[FMA]
A collection of caudal vertebrae in the coccygeal region that are fused and part of the bony pelvis.
Small, bony element consisting of several fused, rudimentary caudal vertebrae; near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle.[AAO]
In humans: The coccyx, commonly referred to as the tailbone, is the final segment of the human vertebral column. Comprising three to five separate or fused vertebrae (the coccygeal vertebrae) below the sacrum, it is attached to the sacrum by a fibrocartilaginous joint, the sacrococcygeal symphysis, which permits limited movement between the sacrum and the coccyx.
The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue.
A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter.
consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct.
tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]
The anus and surrounding regions. Encompasses both internal and external regions, where present
In human anatomy, inferior epigastric artery refers to the artery that arises from the external iliac artery and anastomoses with the superior epigastric artery. Along its course, it is accompanied by a similarly named vein, the inferior epigastric vein. [WP,unvetted].
The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted].
The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted].
The inferior rectal artery (inferior hemorrhoidal artery) is an artery that supplies blood to the lower half of the anal canal. [WP,unvetted].
The perineal artery (superficial perineal artery) arises from the internal pudendal artery, and turns upward, crossing either over or under the Transversus perinæi superficialis, and runs forward, parallel to the pubic arch, in the interspace between the Bulbocavernosus and Ischiocavernosus, both of which it supplies, and finally divides into several posterior scrotal branches which are distributed to the skin and dartos tunic of the scrotum. As it crosses the Transversus perinæi superficialis it gives off the transverse perineal artery which runs transversely on the cutaneous surface of the muscle, and anastomoses with the corresponding vessel of the opposite side and with the perineal and inferior hemorrhoidal arteries. It supplies the Transversus perinæi superficialis and the structures between the anus and the urethral bulb. [WP,unvetted].
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
The deep circumflex iliac vein is formed by the union of the venæ comitantes of the deep iliac circumflex artery, and joins the external iliac vein about 2 cm. above the inguinal ligament. It also receives small tributary branches from the thoracoepigastric vein [WP,unvetted].
In the human body, the femoral vein is a blood vessel that accompanies the femoral artery in the femoral sheath. It begins at the adductor canal (also known as Hunter's canal) and is a continuation of the popliteal vein. It ends at the inferior margin of the inguinal ligament, where it becomes the external iliac vein. [WP,unvetted].
Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO]
The great saphenous vein (GSV), also greater saphenous vein, is the large (subcutaneous) superficial vein of the leg and thigh. The terms 'safaina' (Greek) and 'el safin' (Arabic) have both been claimed as the origin for the word 'saphenous'. [WP,unvetted].
The joint in the bony pelvis between the sacrum and the ilium of the pelvis, which are joined by strong ligaments.
In humans, the sacrum supports the spine and is supported in turn by an ilium on each side
The outer layer of peritoneum that is attached to the abdominal and pelvic walls.
Peritoneum attached to the abdominal wall.[AAO]
The Sphincter ani externus (external anal sphincter) is a flat plane of muscular fibers, elliptical in shape and intimately adherent to the integument surrounding the margin of the anus. [WP,unvetted].
An adductor muscle that attaches to the femur and the pelvis. In humans, the obturator externus muscle is a flat, triangular muscle, which covers the outer surface of the anterior wall of the pelvis. It is sometimes considered part of the medial compartment of thigh, and sometimes considered part of the gluteal region. [WP,generalized].
Originates on the ventro-lateral pelvic rim and inserts on the ventral aspect of the femur, medial to the insertion of the pectineus.[AAO]
the definition generalized to accommodate the AAO class - 'Originates on the ventro-lateral pelvic rim and inserts on the ventral aspect of the femur, medial to the insertion of the pectineus.' [AAO:0010043]
The iliacus is a flat, triangular muscle, which fills the iliac fossa. [WP,unvetted].
AAO has iliacus major and minor, both of which attach to ilium and femur - consider grouping these somehow
The largest and most superficial of the three gluteal muscles [WP,unvetted].
In humans, it makes up a large portion of the shape and appearance of the buttocks. It is a broad and thick fleshy mass of a quadrilateral shape, and forms the prominence of the nates. Its large size is one of the most characteristic features of the muscular system in humans, connected as it is with the power of maintaining the trunk in the erect posture. The muscle is remarkably coarse in structure, being made up of fasciculi lying parallel with one another and collected together into large bundles separated by fibrous septa.
One of three gluteal muscles, is a broad, thick, radiating muscle, situated on the outer surface of the pelvis. Its posterior third is covered by the gluteus maximus, its anterior two-thirds by the gluteal aponeurosis, which separates it from the superficial fascia and integument. [WP,unvetted].
The psoas minor is a long, slender skeletal muscle that, when present, is placed in front of the psoas major muscle. [WP,unvetted].
Human variation notes: It is absent in 40% of individuals.
The Sartorius muscle – the longest muscle in the human body – is a long thin muscle that runs down the length of the thigh. Its upper portion forms the lateral border of the femoral triangle.
The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius.[well established][VHOG]
Taxon notes (via VHOG): "The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius." Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution, Fourth Edition (2006) McGraw-Hill, p.391 [VHOG:0001192]. No iliotibialis in AAO - M. sartorius has def: "Originates on the ventral pelvic rim, the pubic region, and the ventral surface of the adductor longus. The insertion bifurcates distally; the ventral portion attaches to the aponeurosis of the cruralis and the dorsal part attaches to the distal attachment of the gracilis major, the semitendinosus, and to the aponeurosis of the cruralis." [AAO:0010027]. We do NOT group this AAO class here at this stage until further evidence of shared attachments
The biceps femoris is a muscle of the posterior (the back) thigh. As its name implies, it has two parts, one of which (the long head) forms part of the hamstrings muscle group. [WP,unvetted].
The semitendinosus is a muscle in the back of the thigh; it is one of the hamstrings. [WP,unvetted].
The tensor fasciae latae or tensor fasciæ latæ is a muscle of the thigh. [WP,unvetted].
One of the muscles belong to the group consisting of the rectus femoris and the three heads of the vastus (lateralis, medialis, intermedius).
The quadriceps is a collective term for the rectus femoris and the three heads of the vastus (lateralis, medialis, intermedius). [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.391][VHOG]
The Rectus femoris muscle is one of the four quadriceps muscles of the human body. (The others are the vastus medialis, the vastus intermedius, and the vastus lateralis. All four combine to form the quadriceps tendon, which inserts into the patella and continues as the patellar ligament. ) The Rectus femoris is situated in the middle of the front of the thigh; it is fusiform in shape, and its superficial fibers are arranged in a bipenniform manner, the deep fibers running straight down to the deep aponeurosis. [WP,unvetted].
The Vastus lateralis (Vastus externus) is the largest part of the Quadriceps femoris. It arises by a broad aponeurosis, which is attached to the upper part of the intertrochanteric line, to the anterior and inferior borders of the greater trochanter, to the lateral lip of the gluteal tuberosity, and to the upper half of the lateral lip of the linea aspera; this aponeurosis covers the upper three-fourths of the muscle, and from its deep surface many fibers take origin. A few additional fibers arise from the tendon of the Glutæus maximus, and from the lateral intermuscular septum between the Vastus lateralis and short head of the Biceps femoris. The fibers form a large fleshy mass, which is attached to a strong aponeurosis, placed on the deep surface of the lower part of the muscle: this aponeurosis becomes contracted and thickened into a flat tendon inserted into the lateral border of the patella, blending with the Quadriceps femoris tendon, and giving an expansion to the capsule of the knee-joint. [WP,unvetted].
The vastus medialis, often called the 'teardrop' muscle, is a medially located muscle of the quadriceps. [WP,unvetted].
The semimembranosus is a muscle in the back of the thigh. It is the most medial of the three hamstring muscles. [WP,unvetted].
An adductor muscle that attaches to the pelvic bone and the femur. In humans, The pectineus muscle is a flat, quadrangular muscle, situated at the anterior part of the upper and medial aspect of the thigh. It can be classified in the medial compartment of thigh (when the function is emphasized) or the anterior compartment of thigh (when the nerve is emphasized). [WP,generalized].
Originates on the lateral border of the ilium and the anterior margin of the pubis. It inserts on the ventral surface of the femoral shaft.[AAO]
Definition generalized to accommodate AAO class - 'Originates on the lateral border of the ilium and the anterior margin of the pubis. It inserts on the ventral surface of the femoral shaft.' [AAO:0010036]
A muscle that is part of the region of the hindlimb between the pelvis and ankle.
see notes on UBERON:0000978 for possible confusion over the term 'leg'.
muscle of upper or lower hindlimb segment
The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html
TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe
the area of the frontal lobe that is involved with integration of voluntary movements and with speech.[MP]
In human anatomy, the tibialis anterior is a muscle that originates in the upper two-thirds of the lateral surface of the tibia and inserts into the medial cuneiform and first metatarsal bones of the foot. Its acts to invert the foot. It is situated on the lateral side of the tibia; it is thick and fleshy above, tendinous below. This muscle overlaps the anterior tibial vessels and deep peroneal nerve in the upper part of the leg. [WP,unvetted]. The M. tibialis cranialis is a muscle that flexes the tarsometatarsus. It originates on the craniodistal aspect of the femur and proximal tibiotarsus and inserts on the cranial surface of the tarsometarsus[EvoWiki].
A penniform muscle of the lateral front part of the hindlimb responsible for extension of the digits and dorsiflexion of the ankle.
In human anatomy, the peroneus longus (also known as fibularis longus) is a superficial muscle in the lateral compartment of the leg, and acts to evert and plantar flex the ankle. It is situated at the upper part of the lateral side of the leg, and is the most superficial of the three peroneus muscles. It is innervated by the superficial fibular nerve (superficial peroneal nerve). [WP,unvetted].
The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg.
The most superficial calf muscle in the posterior part of the leg. [TFD][VHOG]
The most prominent ventral muscle of the shank is the gastrocnemius, the 'calf' muscle. In mammals, it has two heads, resulting from the fusion of two different phylogenetic predecessors.[well established][VHOG]
In mammals this muscle has two heads[ISBN10:0073040584]
involved in standing, walking, running and jumping
A deep muscle of the triceps surae group, in the superficial posterior compartment of the leg.
responsible for plantar flexion of the foot
The sural arteries (inferior muscular arteries) are two large branches, which are distributed to the Gastrocnemius, Soleus, and Plantaris. The term applies to any of four or five arteries arising from the popliteal artery, with distribution to the muscles and integument of the calf, and with anastomoses to the posterior tibial, medial and lateral inferior genicular arteries. [WP,unvetted].
The popliteus muscle in the leg is used to unlock the knee by laterally rotating the femur on the tibia during a closed chain movement (such as one with the foot in contact with the ground). [WP,unvetted].
A deep muscle of the posterior compartment of the hindlimb that is innervated by the tibial nerve, arises from the fibula and insets in the distal phalanx of pedal digit 1.
The primary auditory cortex is the region of the brain that is responsible for processing of auditory information. [WP,unvetted].
In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery.
axillary part of trunk of subclavian artery
The thoracoacromial artery (acromiothoracic artery; thoracic axis) is a short trunk, which arises from the forepart of the axillary artery, its origin being generally overlapped by the upper edge of the Pectoralis minor. [WP,unvetted].
In human anatomy, the lateral thoracic artery (or external mammary artery) is a blood vessel that supplies oxygenated blood to the lateral structures of the thorax and breast. It originates from the axillary artery and follows the lower border of the Pectoralis minor muscle to the side of the chest, supplies the serratus ventralis muscle and the Pectoralis major muscle, and sends branches across the axilla to the axillary lymph nodes and Subscapularis muscle. It anastomoses with the internal thoracic artery, subscapular, and intercostal arteries, and with the pectoral branch of the thoracoacromial artery. In the female it supplies an external mammary branch which turns round the free edge of the Pectoralis major and supplies the breasts. [WP,unvetted].
The subscapular artery, the largest branch of the axillary artery, arises at the lower border of the Subscapularis, which it follows to the inferior angle of the scapula, where it anastomoses with the lateral thoracic and intercostal arteries and with the descending branch of the transverse cervical, and ends in the neighboring muscles. About 4 cm. from its origin it gives off two branches, first the scapular circumflex artery and then the thoracodorsal artery. [WP,unvetted].
The brachial artery is the major blood vessel of the (upper) arm. It is the continuation of the axillary artery beyond the lower margin of teres major muscle. It continues down the ventral surface of the arm until it reaches the cubital fossa at the elbow. It then divides into the radial and ulnar arteries which run down the forearm. In some individuals, the bifurcation occurs much earlier and the ulnar and radial arteries extend through the upper arm. The pulse of the brachial artery is palpable on the anterior aspect of the elbow, medial to the tendon of the biceps, and, with the use of a stethoscope and sphygmomanometer (blood pressure cuff) often used to measure the blood pressure. The brachial artery is closely related to the median nerve; in proximal regions, the median nerve is immediately lateral to the brachial artery. Distally, the median nerve crosses the medial side of the brachial artery and lies anterior to the elbow joint. [WP,unvetted].
Part of the subclavian artery which supplies blood to the forelimb.[AAO]
brachial part of trunk of subclavian artery
The arteria profunda brachii (also known as deep artery of the arm and the deep brachial artery) is a large vessel which arises from the medial and back part of the brachial, just below the lower border of the Teres major. [WP,unvetted].
The iliocostalis dorsi (musculus accessorius; iliocostalis thoracis) arises by flattened tendons from the upper borders of the angles of the lower six ribs medial to the tendons of insertion of the iliocostalis lumborum; these become muscular, and are inserted into the upper borders of the angles of the upper six ribs and into the back of the transverse process of the seventh cervical vertebra.
The longissimus thoracis is the intermediate and largest of the continuations of the sacrospinalis.[WP]. intermediate erector spinae muscle of back; origin, with iliocostalis and from transverse processes of lower thoracic vertebrae; insertion, by lateral slips into most or all of the ribs between angles and tubercles and into tips of transverse processes of upper lumbar vertebrae, and by medial slips into accessory processes of upper lumbar and transverse processes of thoracic vertebrae; action, extends vertebral column; nerve supply, dorsal primary rami of thoracic and lumbar spinal nerves[Stedmans].
TODO - add logical definition to determine if AAO class belongs here. Classified as erector spinae in AAO
Epaxial muscle which originates on the antero-lateral urostyle and inserts variably along the neural spines and transverse processes of the presacral vertebrae to the exoccipital bone.[AAO]
In human anatomy, the radial artery is the main blood vessel, with oxygenated blood, of the lateral aspect of the forearm. [WP,unvetted].
Origin: spinous processes of two upper lumbar and two lower thoracic; insertion: spines of upper thoracic vertebrae; innervation: branches of spinal nerves; action: extends vertebral column.
The ulnar artery is the main blood vessel, with oxygenated blood, of the medial aspect of the forearm. It arises from the brachial artery and terminates in the superficial palmar arch, which joins with the superficial branch of the radial artery. It is palpable on the anterior and medial aspect of the wrist. Along its course, it is accompanied by a similarly named vein or veins, the ulnar vein or ulnar veins. The ulnar artery, the larger of the two terminal branches of the brachial, begins a little below the bend of the elbow in the cubital fossa, and, passing obliquely downward, reaches the ulnar side of the forearm at a point about midway between the elbow and the wrist. It then runs along the ulnar border to the wrist, crosses the transverse carpal ligament on the radial side of the pisiform bone, and immediately beyond this bone divides into two branches, which enter into the formation of the superficial and deep volar arches. [WP,unvetted].
The Semispinalis dorsi (or semispinalis thoracis) consists of thin, narrow, fleshy fasciculi, interposed between tendons of considerable length. It arises by a series of small tendons from the transverse processes of the sixth to the tenth thoracic vertebræ, and is inserted, by tendons, into the spinous processes of the upper four thoracic and lower two cervical vertebrae. [WP,unvetted].
The semispinalis cervicis (semispinalis colli), thicker than the semispinalis dorsi, arises by a series of tendinous and fleshy fibers from the transverse processes of the upper five or six thoracic vertebræ, and is inserted into the cervical spinous processes, from the axis to the fifth inclusive. The fasciculus connected with the axis is the largest, and is chiefly muscular in structure. [WP,unvetted].
The Semispinalis capitis (Complexus) is situated at the upper and back part of the neck, deep to the Splenius, and medial to the Longissimus cervicis and capitis. It arises by a series of tendons from the tips of the transverse processes of the upper six or seven thoracic and the seventh cervical vertebræ, and from the articular processes of the three cervical above this. The tendons, uniting, form a broad muscle, which passes upward, and is inserted between the superior and inferior nuchal lines of the occipital bone. The medial part, usually more or less distinct from the remainder of the muscle, is frequently termed the Spinalis capitis; it is also named the Biventer cervicis since it is traversed by an imperfect tendinous inscription. [WP,unvetted].
Three common palmar digital arteries arise from the convexity of the superficial palmar arch and proceed distally on the second, third, and fourth lumbricales muscles.
the MA term, even though plural, represents the singular, as it is an isa child of artery
A superficial vein of the upper limb that drain parts of manus and forearm.
It originates on the medial (ulnar) side of the dorsal venous network of the manus, and it travels up the base of the forearm and arm. Most of its course is superficial; it generally travels in the subcutaneous fat and other fasciae that lie superficial to the muscles of the upper extremity. Because of this, it is usually visible through the skin. Near the region anterior to the cubital fossa, in the bend of the elbow joint, the basilic vein usually connects with the other large superficial vein of the upper extremity, the cephalic vein, via the median cubital vein. The layout of superficial veins in the forearm is highly variable from person to person, and there are generally a variety of other unnamed superficial veins that the basilic vein communicates with. About halfway up the arm proper (the part between the shoulder and elbow), the basilic vein goes deep, travelling under the muscles. There, around the lower border of the teres major muscle, the anterior and posterior circumflex humeral veins feed into it, just before it joins the brachial veins to form the axillary vein. Along with other superficial veins in the forearm, the basilic vein is a possible site for venipuncture.
Some sources distinguish between the "proper palmar digital veins", which are more distal, and the "common palmar digital veins", which are more proximal.
In human anatomy, the brachial veins are venae comitantes of the brachial artery in the arm proper. Because they are deep to muscle, they are considered deep veins. Their course is that of the brachial artery (in reverse): they begin where radial veins and ulnar veins join (corresponding to the bifurcation of the brachial artery). They end at the inferior border of the teres major muscle. At this point, the brachial veins join the basilic vein to form the axillary vein. The brachial veins also have small tributaries that drain the muscles of the upper arm, such as biceps brachii muscle and triceps brachii muscle. [WP,unvetted].
Vein which collects blood from the forelimb and drains into the subclavian vein.[AAO]
In human anatomy, the median cubital vein (or median basilic vein) a superficial vein of the upper limb. It connects the basilic and cephalic vein and is often used for venipuncture (taking blood). It lies in the cubital fossa superficial to the bicipital aponeurosis. There exists a fair amount of variation of the median cubital vein. More commonly the vein forms an H-pattern with the cephalic and basilic veins making up the sides. Other forms include an M-pattern, where the vein branches to the cephalic and basilic veins. [WP,unvetted].
A zone of skin that is part of a pelvis [Automatically generated definition].
A zone of skin that is part of an abdomen [Automatically generated definition].
A zone of skin that is part of a neck [Automatically generated definition].
A zone of skin that is part of a thorax [Automatically generated definition].
A zone of skin that is part of a limb [Automatically generated definition].
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]
Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]
A lymphatic vessel that is part of a face [Automatically generated definition].
The major preaxial endochondral bone in the anterior zeugopod[Phenoscape].
One of the two long bones of endochondral origin of the fore-epipodium; it is located on the lateral side of the ulna. Its upper end articulates with both the humerus and the ulna, whereas the lower articulates with the carpals.[AAO]
Due to the presence of the radius in Tetrpodomorph fish this element is not inherently linked to the presence of digits or flexor musculature. The corresponding bone in the posterior fin/limb is the tibia.[Phenoscape]. In four-legged animals, the radius is the main load-bearing bone of the lower forelimb. Its structure is similar in most terrestrial tetrapods, but it may be fused with the ulna in some mammals (such as horses) and reduced or modified in animals with flippers or vestigial forelimbs [ISBN:0-03-910284-X]
The major postaxial endochondral bone in the anterior zeugopod[Phenoscape].
One of the two long bones of endochondral origin of the fore-epipodium; it is located on the medial (inner) side of the radius. The upper end of the ulna articulates with the lower end of the humerus forming a strong hinge joint with the carpals, whereas the lower articulates with the carpals.[AAO]
The corresponding bone in the posterior fin/limb is the fibula.
the bone of the hand located at the radial side of the carpus and which articulates with the radius, trapezium, trapezoideum, capitate, and lunate bones
TODO - check AAO placement; in rodents this is fused with the lunate to make the scapholunate
One of two element that constitute the basal row of carpals. It articulates proximally with the radius, mesially with the ulnare (or pars intermedia of the ulnare when the ulnare is fused to the intermedium) and distally with the centrale (also recognized by some authors as element Y). This element originates from one or two condensation centers. Occasionally it may fuse to carpal 5(4), the ulnare, or other elements.[AAO]
In reptiles, birds, and amphibians, this bone is instead commonly referred to as the radiale, because of its articulation with the radius[WP]
The lunate bone (semilunar bone) is a carpal bone (wrist bone) in the human hand that may be distinguished by its deep concavity and crescentic outline. It is situated in the center of the proximal row of the carpus (wrist) region between the fore arm and hand (manus). In standard medical posture, the lunate carpal bone is situated between the lateral Scaphoid bone and medial Triquetral bone. The lunate carpal bone straddles distally the bordering ulna and radius bones and proximally to distal carpus (wrist) Trapezium bone and Trapezoid bone[WP].
articulating with the ulnare and the radiale[VSAO]. human articulations: radius proximally capitate and hamate distally scaphoid laterally triangular medially
A laterally positioned sesamoid bone found in close proximity with and occasionally fused to the ulnare.
located between radiale and first metacarpal[VSAO]. in humans - The capitate articulates with 1st metacarpal distally, scaphoid proximally, trapezoid medially, 2nd metacarpal medially
Small element that articulates with the prepollex, metacarpal II(I) and metacarpal III(II). It may be fused to element Y or carpal 3(2).[AAO]
The trapezoid bone (lesser multangular bone) is a carpal bone in tetrapods, including humans. It is the smallest bone in the distal row. It may be known by its wedge-shaped form, the broad end of the wedge constituting the dorsal, the narrow end the palmar surface; and by its having four articular facets touching each other, and separated by sharp edges. It is homologous with the 'second distal carpal' of reptiles and amphibians. The etymology derives from the Greek trapezion which means 'irregular quadrilateral,' from tra- 'four' and peza 'foot' or 'edge. ' Literally, 'a little table' from trapeza meaning 'table' and -oeides 'shaped.[Wikipedia:Trapezoid_bone]
located in the distal part of the carpus and articulating with the second metacarpal, the distal carpals 1 and 2 and the radiale.[VSAO] in humans - The capitate articulates with 2nd metacarpal distally, scaphoid proximally, trapezium medially, capitate medially[WP] Amphibians: Small element that articulates with the prepollex, metacarpal II(I) and metacarpal III(II). It may be fused to element Y or carpal 3(2)
Small element that articulates anteriorly with metacarpal III(II). It may be fused to carpals 2(1), 4(3), 5(4), or other elements.[AAO]
medially located and articulates with metacarpals 2-4, distal carpal 5 and the intermedium[VSAO] In the human hand, the capitate bone is the largest of the carpal bones, and occupies the center of the wrist - The capitate articulates with seven bones: the scaphoid and lunate proximally, the second metacarpal, third metacarpal, and fourth metacarpal distally, the lesser multangular on the radial side, and the hamate on the ulnar side
Small element that articulates anteriorly with metacarpal IV(III). It may be fused to carpal 3(2), 5(4), or other elements.[AAO]
articulates with the lunar, distal carpal 3, the ulnare as well as metacarpals 4 and 5.[VSAO]. In the human hand the lunate proximally the fourth and fifth metacarpals distally the triangular medially the capitate laterally[WP] Amphibians: Small element that articulates anteriorly with metacarpal IV(III). It may be fused to carpal 3(2), 5(4), or other elements
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm].
In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist.
A phalanx that is part of a forelimb autopod[Automatically generated definition].
Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO]
Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur.[FMA]
Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO]
Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]
todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA.
the outer layers of solid, hard bone that covers spongy bone; consists of parallel osteons containing mineral deposits and interstitial lamellae
MP distinguishes compact/cortical bone. in other AOs they are syns
The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle
TODO - find a home for: FMA:24139 ! skeleton of upper limb
Skeletal structure of the paired, anterior appendages.[AAO]
Subdivision of skeleton consisting of all skeletal elements in an hindlimb region.
Skeletal structure of the paired, posterior appendages.[AAO]
Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape].
here 'manus' includes both the wrist region, metatarsal region and acropodial region
Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA].
FMA:24216 present in FMA1, but gone in subsequent versions
Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape].
here 'pes' includes both the ankle region, metatarsals and acropodial region
The major postaxial endochondral bone in the posterior zeugopod[Phenoscape].
One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO]
A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia.
In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment
The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted].
A phalanx that is part of a hindlimb autopod[Automatically generated definition].
Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO]
The postaxial bone of the proximal tarsals series[Phenoscape].
synonymous with the fibulare of basal tetrapods.
the oval-shaped tarsal bone found between the talus and the 3 cuneiform bones
Oval tarsal element that is located on the center of the mesopodium. It articulates with all other elements of the tarsus except tarsal 5.[AAO]
connections vary depending on species. AAO: Oval tarsal element that is located on the center of the mesopodium. It articulates with all other elements of the tarsus except tarsal 5. In humans: there is a cuboid instead of distal tarsal 4 and 5 - may articulate laterally with the cuboid
Endochondral tarsal bone articulating with centralia and metatarsal 1.
Small element that articulates with the prehallux, metatarsal I and element Y. It may be fused to tarsal 2.[AAO]
Endochondral tarsal bone articulating with centralia and metatarsal 2.
Small element that articulates anteriorly with metatarsal II. It may be fused to tarsal 1 or to tarsal 3.[AAO]
The intermediate cuneiform (also known as second cuneiform / middle cuneiform) is shaped like a wedge, the thin end pointing downwards. It is situated between the other two cuneiforms (the medial and lateral cuneiforms), and articulates with the navicular posteriorly, the second metatarsal anteriorly and with the other cuneiforms on either side. [WP,unvetted]
Endochondral tarsal bone articulating with centralia and metatarsal 3.
Small element that articulates anteriorly with metatarsal III. It may be fused to tarsal 2.[AAO]
In some types, the cuneiform is found as two or three bones, in which case the more anterior ('dorsal' in dorsal/plantar terminology) is the ectocuneiform, while the more posterior or plantar bones are the mesocuneiform and entocuneiform.[Palaeos]
The lateral cuneiform (also known as third cuneiform / external cuneiform) intermediate in size between the other two cuneiform bones, is also wedge-shaped, the base being uppermost. It occupies the center of the front row of the tarsal bones, between the second cuneiform medially, the cuboid laterally, the navicular posteriorly and the third metatarsal in front. [WP,unvetted]
A tarsal bone that is formed from distal tarsals 4 and 5. [WP,modified].
NominaAnatomicaVeterinaria uses os cuboideum as an official synonym for distal tarsal IV, but some sources also use this as the label for the human cuboid bone which is regarded to be formed from tarsals IV and V. We therefore decline to use exact syns in either case.
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and olfactory apparatus (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
A zone of skin that is part of a eyelid [Automatically generated definition].
A zone of skin that is part of a lip [Automatically generated definition].
A zone of skin that is part of a external ear [Automatically generated definition].
zone of skin of auricular region of head
The part of the forelimb extending from the shoulder to the autopod[cjm].
currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand
this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm
The elbow is the region surrounding the elbow-joint—the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific].
1st (preaxial) digit of the manus[Wikipedia].
Not present in Anurans (Phenotype RCN Oct 2012)
This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit).
The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified].
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint
A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.
pedal digit (phalangeal portion) plus soft tissue
A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).
(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]
In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone
The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments.
FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra
The sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted].
The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted].
note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship
in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle
the loose fold of skin that covers the penis
A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO].
A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]
A vessel that contains or conveys lymph.[AAO]
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
made obsolete as it incorrectly grouped classes
A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized]
Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO]
We use a generic definition that includes the deltoideus as represented in AAO: 'Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus'. Kardong: Dorsal group
The infraspinatus muscle is a thick triangular muscle, which occupies the chief part of the infraspinatous fossa. The infraspinatus is a muscle of the rotator cuff. [WP,unvetted].
The pectoral muscles — the pectoralis major and pectoralis minor — evolved from a primitive muscle sheet that connected the coracoid to the humerus. In late reptilians and early mammals, this muscle structure was displaced dorsally; while most of its components evolved into the pectoralis major, some fibers eventually attached to the scapula and evolved into the supraspinatus, the infraspinatus, and parts of the subscapularis.
Teres major is a muscle of the upper limb and one of six scapulohumeral muscles. It is a thick but somewhat flattened muscle. [WP,unvetted].
A sesamoid element that is composed of bone tissue.
Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.[VSAO]
A carpal bone that proximally_connected_to a forelimb zeugopod skeleton.
A distal carpal endochondral element that is composed primarily of a bone tissue.
Series of elements that articulate with the metacarpals.[AAO]
Primitively, each of the distal bones appears to have articulated with a single metacarpal
A muscle organ that is part of a shoulder [Automatically generated definition].
A zone of skin that is part of a shoulder region.
in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted].
A synovial joint that connects the femur to the acetbulum of the innominate bone.
A skeletal joint that is part of a pes [Automatically generated definition].
TODO check FMA - use the set class for now
joint of terminal segment of free lower limb
A joint that connects the hindlimb autopod and zeugopod skeletons.
todo - accurately represent different types of ankle joint
A skeletal joint that is part of a manus (hand) [Automatically generated definition].
joint of terminal segment of free upper limb
A joint that connects the forelimb zeugopod and stylopod skeletons[Obol].
In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis
A joint connecting the forelimb zeugopod skeleton with the carpal skeleton.
in FMA this includes radio-carpal and radio-ulnar *ligaments*
The radial nerve is a nerve in the human body that supplies the upper limb. It supplies the triceps brachii muscle of the arm, as well as all 12 muscles in the posterior osteofascial compartment of the forearm, as well as the associated joints and overlying skin. It originates from the posterior cord of the brachial plexus with roots from C5, C6, C7, C8 & T1. The radial nerve and its branches supply the dorsal muscles, such as triceps brachii, the extrinsic extensors of the wrist and hands, and the cutaneous nerve supply to most of the back of the hand. (The ulnar nerve cutaneously innervates the back of the little finger and adjacent half of the ring finger). The radial nerve divides into a deep branch (which becomes the posterior interosseous nerve), and continues as the superficial branch which goes on to innervate the dorsum (back) of the hand. [WP,unvetted].
The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted].
In human anatomy, the ulnar nerve is a nerve which runs near the ulna bone. The ulnar nerve is the largest unprotected nerve in the human body (meaning, unprotected by muscle or bone), and the only unprotected nerve that does not serve a purely sensory function (those nerves specifically meant to perceive changes in the environment, such as nerves in the skin). This nerve is directly connected to the little finger, and the adjacent half of the ring finger, supplying the palmar side of these fingers, including both front and back of the tips, perhaps as far back as the fingernail beds. One method of injuring the nerve is to strike the medial epicondyle of the humerus from posteriorly, or inferiorly with the elbow flexed. The ulnar nerve is trapped between the bone and the overlying skin at this point. This is commonly referred to as hitting one's 'funny bone. ' This name is thought to be a pun, based on the sound resemblance between the words 'humerus' and 'humourous' . [WP,unvetted].
Muscles of the upper chest. The term may refer to one of two muscles, the pectoralis major and pectoralis minor. The former is a thick muscle in the anterior portion of the chest. Its action involves flexion, medial rotation, and adduction of the humerus. The latter is a thin muscle located beneath the pectoralis major. Its action involves lowering the scapula and raising the ribs.
Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus.[AAO]
This currently groups the major and minor muscles (which have different attachment sites) as well as the AAO structure: Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart’s axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]
A muscle organ that is part of a pelvic girdle [Automatically generated definition].
Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.
A muscle organ that is part of a pes [Automatically generated definition].
distal free limb segment of hind limb muscle organ
distal free limb segment of hindlimb muscle organ
distal free limb segment of inferior member muscle organ
distal free limb segment of lower extremity muscle organ
hind limb distal free limb segment muscle organ
hindlimb distal free limb segment muscle organ
inferior member distal free limb segment muscle organ
lower extremity distal free limb segment muscle organ
muscle organ of autopod of inferior member
muscle organ of autopod of lower extremity
muscle organ of distal free limb segment of hind limb
muscle organ of distal free limb segment of hindlimb
muscle organ of distal free limb segment of inferior member
muscle organ of distal free limb segment of lower extremity
muscle organ of hind limb distal free limb segment
muscle organ of hindlimb distal free limb segment
muscle organ of inferior member distal free limb segment
muscle organ of lower extremity distal free limb segment
muscle organ of terminal segment of free lower limb
terminal segment of free lower limb muscle organ
A muscle organ that is part of an arm [Automatically generated definition].
See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)
A muscle organ that is part of a manus [Automatically generated definition].
arm distal free limb segment muscle organ
autopod of proximal segment of free upper limb muscle organ
brachial region distal free limb segment muscle organ
distal free limb segment of arm muscle organ
distal free limb segment of brachial region muscle organ
distal free limb segment of proximal segment of free upper limb muscle organ
muscle organ of arm distal free limb segment
muscle organ of autopod of brachial region
muscle organ of autopod of proximal segment of free upper limb
muscle organ of brachial region distal free limb segment
muscle organ of distal free limb segment of arm
muscle organ of distal free limb segment of brachial region
muscle organ of distal free limb segment of proximal segment of free upper limb
muscle organ of proximal segment of free upper limb autopod
muscle organ of proximal segment of free upper limb distal free limb segment
muscle organ of terminal segment of free upper limb
proximal segment of free upper limb autopod muscle organ
proximal segment of free upper limb distal free limb segment muscle organ
terminal segment of free upper limb muscle organ
The lumbricals are intrinsic muscles of the manus that flex the metacarpophalangeal joints and extend the interphalangeal joints
An interosseous muscle that is part of a manus.
The interosseous muscles are flexor muscles of the manus that help support and flex the metacarpophalangeal joints. In some species the muscles are known as the suspensory ligaments. The muscles are found under the deep digital flexor tendon and originate from the base of each metacarpal bone. From its origin each muscle runs a short way down until it divides into two tendons that continue down and insert onto the base of its corresponding proximal phalanx. Each tendon has a sesamoid imbedded within it, that lie over the metacarpophalangeal joint. A small tendon, sometimes known as an extensor branch, continues to proceed from the base of each proximal phalanx and connects to the common extensor tendon. It has a small role to play in the extension of each phalanx. The main innervation of this muscle is via a branch of the ulnaris nerve[MURDOCH:1022].
The dorsal interossei of the hand are muscles that occupy the space between the metacarpals. There are four dorsal interossei in each hand. They are specified as 'dorsal' to contrast them with the palmar interossei, which are located on the anterior side of the metacarpals. The dorsal interosseous muscles are bipennate, with each muscle arising by two heads from the adjacent sides of the metacarpal bones, but more extensively from the metacarpal bone of the finger into which the muscle is inserted. They are inserted into the bases of the proximal phalanges and into the extensor expansion of the corresponding extensor digitorum tendon. The middle digit has two dorsal interossei insert onto it while the first digit (thumb) and the fifth digit (little finger) have none[WP].
The lumbricals are four small skeletal muscles, accessory to the tendons of the flexor digitorum longus and numbered from the medial side of the pes; they arise from these tendons, as far back as their angles of division, each springing from two tendons, except the first.
The Coracobrachialis is the smallest of the three muscles that attach to the coracoid process of the scapula. (The other two muscles are pectoralis minor and biceps brachii. ) It is situated at the upper and medial part of the arm. It is perforated by and innervated by the musculocutaneous nerve. [WP,unvetted].
The brachialis (brachialis anticus) is a muscle in the upper arm that flexes the elbow joint. It lies just deep of the biceps brachii, and is a synergist that assists the biceps brachii in flexing at the elbow. It makes up part of the floor of the region known as the cubital fossa. [WP,unvetted].
A muscle of the stylopodium, covering the distal half of the humerus and the anterior part of the elbow joint. It functions to flex the zeugopodium. [TFD][VHOG]
A muscle in the forelimb stylopod which in humans has several functions, the most important being to rotate the forearm and to flex the elbow. [WP,unvetted].
the convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery
The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]
The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]
birds have right aortic arch, mammals left.
The triceps brachii muscle (Latin for 'three-headed' muscle of the arm, it is called a three headed muscle because there are three bundles of muscle, each of different origin, joining together at the elbow) is the large muscle on the back of the human upper limb. It is the muscle principally responsible for extension of the elbow joint (i.e. straightening of the arm). Though a similarly-named muscle, the triceps surae, is found on the lower leg, the triceps brachii is commonly called simply the 'triceps'. [WP,unvetted].
Dorsal group derivative that acts on the forearm[Kardong]
A zone of skin that is part of a knee [Automatically generated definition].
A zone of skin that is part of a leg [Automatically generated definition].
A zone of skin that is part of an ankle [Automatically generated definition].
A zone of skin that is part of a pes [Automatically generated definition].
distal free limb segment of hind limb zone of skin
distal free limb segment of hindlimb zone of skin
distal free limb segment of inferior member zone of skin
distal free limb segment of lower extremity zone of skin
hind limb distal free limb segment zone of skin
hindlimb distal free limb segment zone of skin
inferior member distal free limb segment zone of skin
lower extremity distal free limb segment zone of skin
terminal segment of free lower limb zone of skin
zone of skin of autopod of inferior member
zone of skin of autopod of lower extremity
zone of skin of distal free limb segment of hind limb
zone of skin of distal free limb segment of hindlimb
zone of skin of distal free limb segment of inferior member
zone of skin of distal free limb segment of lower extremity
zone of skin of hind limb distal free limb segment
zone of skin of hindlimb distal free limb segment
zone of skin of inferior member distal free limb segment
zone of skin of lower extremity distal free limb segment
zone of skin of terminal segment of free lower limb
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
results from fusion of left and right dorsal aortae
the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
A zone of skin that is part of a elbow [Automatically generated definition].
A zone of skin that is part of a wrist [Automatically generated definition].
A zone of skin that is part of a manus [Automatically generated definition].
The pronator teres is a muscle of the human body (located mainly in the forearm) that, along with the pronator quadratus, serves to pronate the forearm (turning it so the palm faces posteriorly). [WP,unvetted].
A muscle of the forearm that acts to flex and abduct the manus. [WP,unvetted].
Muscle which originates on the inner border of the humerus and inserts on the carpus.[AAO]
we group the AAO class here, despite the different insertion site - requires vetting: Muscle which originates on the inner border of the humerus and inserts on the carpus. [AAO:0010733]
The flexor carpi ulnaris muscle (FCU) is a muscle of the human forearm that acts to flex and adduct the manus. [WP,unvetted].
AAO has a class with the same name, the exact insertion point is unclear; consider grouping :Muscle which originates from the medial condyle of the humerus and inserts on the carpus. [AAO:0010734]
A muscle in the forearm that flexes the manual digits[WP,modified].
in EMAPA, this is part of the leg, which is presumably a mistake
Extensor carpi radialis longus is one of the five main muscles that control movements at the wrist. This muscle is quite long, starting on the lateral side of the humerus, and attaching to the base of the second metacarpal bone (metacarpal of the index finger). [WP,unvetted].
The Extensor carpi radialis brevis is shorter and thicker than the extensor carpi radialis longus. The longus muscle can be found above the distal end of the Extensor carpi radialis brevis. [WP,unvetted].
Extensor carpi ulnaris is a muscle located in the forearm that acts to extend and adduct the wrist. Being an extensor muscle, extensor carpi ulnaris is on the posterior side of the forearm. [WP].
Note that we make the insertion relationship a taxon GCI until digit numbering issues are resolved
Muscle of the forearm: It shares a common origin with two other muscles of the forearm. It arises from the lateral epicondyle of the humerus by two tendons: the first one is in common with the m. extensor digitorum communis longus, and the second one is broad and in common with the m. epicondylocubitalis. It is pinnately attached to the dorsal surface of the distal carpal 5-4-3.[AAO]
The Abductor pollicis longus lies immediately below the Supinator and is sometimes united with it. [WP,unvetted].
A joint that connects the radius and the ulna. Examples: proximal and distal radio-ulnar joints
the short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
In human anatomy, the common carotid artery is an artery that supplies the head and neck with oxygenated blood; it divides in the neck to form the external and internal carotid arteries. [WP,unvetted].
placement of the MA class here is not strictly correct, as the MA class does not include the branches
right common carotid artery plus branches
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP]
Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG]
One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO]
One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta
Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)
Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]
In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]
The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]
The subclavian artery that supplies the right pectoral appendage
in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery
proximal part arises from right 4th aortic arch in humans
the first branch of the left and right subclavian arteries that merge to form the single midline basilar artery; branches of the vertebral arteries supply the musculature of the neck
The two vertebral arteries and the basilar artery are sometimes together called the vertebrobasilar system, which supplies blood to the posterior part of circle of Willis and anastomoses with blood supplied to the anterior part of the circle of Willis from the carotid arteries. [WP,unvetted]
left common carotid artery plus branches
The anterior tibial artery of the lower limb carries blood to the anterior compartment of the leg and dorsal surface of the foot, from the popliteal artery. It is accompanied by a deep vein, the anterior tibial vein, along its course. It crosses the anterior aspect of the ankle joint, at which point it becomes the dorsalis pedis artery. [WP,unvetted].
The posterior tibial artery of the lower limb carries blood to the posterior compartment of the leg and plantar surface of the foot, from the popliteal artery. It is accompanied by a deep vein, the posterior tibial vein, along its course. [WP,unvetted].
In human anatomy, the dorsalis pedis artery (dorsal artery of foot), is a blood vessel of the lower limb that carries oxygenated blood to the dorsal surface of the foot. It arises at the anterior aspect of the ankle joint and is a continuation of the anterior tibial artery. It terminates at the proximal part of the first intermetatarsal space, where it divides into two branches, the first dorsal metatarsal artery and the deep plantar artery. Along its course, it is accompanied by a deep vein, the dorsalis pedis vein. [WP,unvetted].
In anatomy, the fibular artery (also known as the peroneal artery) supplies blood to the lateral compartment of the leg and is typically a branch of posterior tibial artery. [WP,unvetted].
The medial plantar artery (internal plantar artery), much smaller than the lateral, passes forward along the medial side of the foot. It is at first situated above the Abductor hallucis, and then between it and the Flexor digitorum brevis, both of which it supplies. At the base of the first metatarsal bone, where it is much diminished in size, it passes along the medial border of the first toe, anastomosing with the first dorsal metatarsal artery. Small superficial digital branches accompany the digital branches of the medial plantar nerve and join the plantar metatarsal arteries of the first three spaces. [WP,unvetted].
the lymph nodes located in the groin area
the lymph nodes which drain the legs; contained in the popliteal fossa
In the popliteal fossa between biceps femoris m. and semitendinosus m..
The popliteal vein course runs alongside the popliteal artery but carries the blood from the knee joint and muscles in the thigh and calf back to the heart. Its origin is defined by the junction of the posterior tibial vein and anterior tibial vein. It drains the peroneal vein before reaching the knee joint and turns into the femoral vein when leaving the adductor canal (also known as Hunter's canal). The popliteal artery extends from the femoral artery behind the popliteal fossa which is the space behind the knee. [WP,unvetted].
In human anatomy, the anterior tibial vein of the lower limb carries blood from the anterior compartment of the leg to the popliteal vein which is forms when it joins with the posterior tibial vein. Like most deep veins, the anterior tibial vein is accompanied by an artery of the same name, the anterior tibial artery, along its course. [WP,unvetted].
In anatomy, the posterior tibial vein of the lower limb carries blood from the posterior compartment and plantar surface of the foot to the popliteal vein which it forms when it joins with the anterior tibial vein. Like most deep veins, the posterior tibial vein is accompanied by an artery of the same name, the posterior tibial artery, along its course. [WP,unvetted].
The small saphenous vein (also lesser saphenous vein), is a relatively large vein of the superficial posterior leg. [WP,unvetted].
The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted].
The term 'sural veins' is not sufficient to appropriately designate the complex venous system of the calf. This should be designated as soleal veins (venae solealis), the veins of the soleus muscle and gastrocnemius veins (venae gastrocnemii)
One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries.
A zone of skin that is part of a hip region.
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
Subdivision of urinary system which consists of the urinary bladder and the urethra.
Subdivision of respiratory system which consists of the nose, nasopharynx, oropharynx and larynx[FMA]
Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage.[WP]
The segment of respiratory tract from the trachea to the lungs[WP,modified]
The subcostal arteries, so named because they lie below the last ribs, constitute the lowest pair of branches derived from the thoracic aorta, and are in series with the intercostal arteries. Each passes along the lower border of the twelfth rib behind the kidney and in front of the Quadratus lumborum muscle, and is accompanied by the twelfth thoracic nerve. It then pierces the posterior aponeurosis of the Transversus abdominis, and, passing forward between this muscle and the Obliquus internus, anastomoses with the superior epigastric, lower intercostal, and lumbar arteries. Each subcostal artery gives off a posterior branch which has a similar distribution to the posterior ramus of an intercostal artery. [WP,unvetted].
A group of muscles (or in some classifications, muscle bellies) that are located under the jaw and attach to the base of the cranium and typically attaches to the hyoid apparatus via a common tendon.
this class refers to the mereological sum of digastric muscles in an organism (typically two).
The digastric muscle (also digastricus) (named digastric as it has two bellies) is a small muscle located under the jaw. It lies below the body of the mandible, and extends, in a curved form, from the mastoid process to the symphysis menti. It belongs to the suprahyoid muscles group. A broad aponeurotic layer is given off from the tendon of the digastricus on either side, to be attached to body and greater cornu of the hyoid bone; this is termed the suprahyoid aponeurosis. http://en.wikipedia.org/wiki/Digastric_muscle].
In most mammals there is a common tendon between the ant. and post. muscles, which also makes a connection to the hyoid apparatus, and then the other attachment is to the base of the cranium
A muscle that arises by four tendinous slips from the transverse processes of the third, fourth, fifth, and sixth cervical vertebrae and inserts into the inferior surface of the basilar part of the occipital bone.[WP,modified].
flexion of neck at atlanto-occipital joint
The mylohyoid is a pharyngeal arch I muscle that participates in oral/pharyngeal behaviors and is innervated by the nerve to mylohyoid and attaches to the midline raphe linking right and left mylohyoid and the mandible.
The mylohyoid is a pharyngeal arch I muscle that participates in oral/pharyngeal behaviors and is innervated by the nerve to mylohyoid and attaches to the midline raphe linking R and L mylohyoid and the mandible.[FEED]
Taxon motes: mylohyoideus and digastricus anterior of rats derived from intermandibularis posterior, see e.g. Jarvik [53] http://www.biomedcentral.com/1471-213X/8/24/table/T3
The geniohyoid is a muscle that attaches to the mandible and the hyoid apparatus and is innervated by the first cervical nerve (C1).
The geniohyoid is a muscle that attaches to the mandible and the hyoid apparatus and is innervated by C1.[FEED]
The cricothyroid muscle attaches to the anterolateral aspect of the cricoid and the inferior cornu and lower lamina of the thyroid cartilage, tilting the thyroid forwards and tensing the vocal cords. It is the only laryngeal muscle supplied by the external branch of the superior laryngeal nerve (rather than the recurrent laryngeal nerve). [WP,unvetted].
A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.
Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO]
In many animals the inside of the cheek is lined with mucous membrane covered with stratified squamous epithelium and supplied with secretions from buccal glands.
TODO - evaluate taxonomic specificity - functional definition?
The inferior pharyngeal constrictor, the thickest of the three constrictors, arises from the sides of the cricoid and thyroid cartilage. Similarly to the superior and middle pharyngeal constrictor muscles, it is innervated by the vagus nerve (cranial nerve X), specifically, by branches from the pharyngeal plexus and by neuronal branches from the recurrent laryngeal nerve. [WP,unvetted].
This is a pharyngeal arch 4/6 muscle that is integral to the pharyngeal tube, participates in oral/pharyngeal behaviors, is innervated by the pharyngeal plexus of the vagus n. and attaches to the laryngeal cartilages and the midline raphe.[FEED]
Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue.
Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG]
Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO]
relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]
The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]
Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.
A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII
Makes up part of the tongue in frogs and salamanders.[AAO]
The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED]
The Styloglossus, the shortest and smallest of the three styloid muscles, arises from the anterior and lateral surfaces of the styloid process, near its apex, and from the stylomandibular ligament. Passing downward and forward between the internal and external carotid arteries, it divides upon the side of the tongue near its dorsal surface, blending with the fibers of the Longitudinalis inferior in front of the Hyoglossus; the other, oblique, overlaps the Hyoglossus and decussates with its fibers. [WP,unvetted].
Styloglossus is a muscle that attaches to the tongue and stylohyal and is innervated by Cranial Nerve XII.[FEED]
The palatoglossus, glossopalatinus, or palatoglossal muscle is a small fleshy fasciculus, narrower in the middle than at either end, forming, with the mucous membrane covering its surface, the glossopalatine arch. It arises from the anterior surface of the soft palate, where it is continuous with the muscle of the opposite side, and passing downward, forward, and lateralward in front of the palatine tonsil, is inserted into the side of the tongue, some of its fibers spreading over the dorsum, and others passing deeply into the substance of the organ to intermingle with the Transversus linguæ. [WP,unvetted].
Palatoglossus is a muscle that attaches to the soft palate and the tongue and is innervated by Cranial Nerve X via the pharyngeal plexus.[FEED]
A muscle organ that attaches the tongue to some other structure.
main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement
All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus.
The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII.
The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED]
The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone
A circumorbital muscle in the face that closes the eyelid[HP].
It arises from the nasal part of the frontal bone, from the frontal process of the maxilla in front of the lacrimal groove, and from the anterior surface and borders of a short fibrous band, the medial palpebral ligament. From this origin, the fibers are directed lateralward, forming a broad and thin layer, which occupies the eyelids or palpebræ, surrounds the circumference of the orbit, and spreads over the temple, and downward on the cheek. The palpebral portion of the muscle is thin and pale; it arises from the bifurcation of the medial palpebral ligament, forms a series of concentric curves, and is inserted into the lateral palpebral raphé. The orbital portion is thicker and of a reddish color; its fibers form a complete ellipse without interruption at the lateral palpebral commissure; the upper fibers of this portion blend with the Frontalis and Corrugator. The lacrimal part (Tensor tarsi) is a small, thin muscle, about 6 mm. in breadth and 12 mm. in length, situated behind the medial palpebral ligament and lacrimal sac. It arises from the posterior crest and adjacent part of the orbital surface of the lacrimal bone, and passing behind the lacrimal sac, divides into two slips, upper and lower, which are inserted into the superior and inferior tarsi medial to the puncta lacrimalia; occasionally it is very indistinct. [WP,unvetted]. [Wikipedia:Orbicularis_oculi_muscle]
Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos].
Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO]
Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787].
The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640].
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]
connects to main OB (in taxa where main/accessory distinction is important)
The levator labii superioris (or quadratus labii superioris) is a broad sheet, the origin of which extends from the side of the nose to the zygomatic bone. Its medial fibers form the angular head, which arises by a pointed extremity from the upper part of the frontal process of the maxilla and passing obliquely downward and lateralward divides into two slips. One of these is inserted into the greater alar cartilage and skin of the nose; the other is prolonged into the lateral part of the upper lip, blending with the infraorbital head and with the Orbicularis oris. The intermediate portion or infraorbital head arises from the lower margin of the orbit immediately above the infraorbital foramen, some of its fibers being attached to the maxilla, others to the zygomatic bone. Its fibers converge, to be inserted into the muscular substance of the upper lip between the angular head and the Caninus. The lateral fibers, forming the zygomatic head, arise from the malar surface of the zygomatic bone immediately behind the zygomaticomaxillary suture and pass downward and medialward to the upper lip. [WP,unvetted].
A muscle of facial expression, innervated by the facial nerve, attached to the skin of the lower lip, orbicularis oris muscle, and mandible, and superficial and lateral to the mentalis muscle. See Diogo et al., 2009; Burrows et al., 2011)
The buccinator is a muscle that is attached to the mandible, skin, pterygomandibular raphe and maxilla, and is innervated by Cranial Nerve VII and participates in oropharyngeal behavior.
Auricular muscle attaching the cartilage of the ear to the epicranial aponeurosis. The 3 extrinsic auricular muscles in humans are: anterior auricular muscle superior auricular muscle posterior auricular muscle [WP,modified].
Wikipedia topic refers to the extrinsic auricular muscles
The subclavian artery that supplies the left pectoral appendage
in humans, branches off the arch of aorta
arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans
A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart.
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
The subclavian vein is a paired large vein, one on either side of the body. Their diameter is approximately that of the smallest finger.
Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO]
The vertebral vein is formed in the suboccipital triangle, from numerous small tributaries which spring from the internal vertebral venous plexuses and issue from the vertebral canal above the posterior arch of the atlas. They unite with small veins from the deep muscles at the upper part of the back of the neck, and form a vessel which enters the foramen in the transverse process of the atlas, and descends, forming a dense plexus around the vertebral artery, in the canal formed by the foramina transversaria of the cervical vertebrae. This plexus ends in a single trunk, which emerges from the foramen transversarium of the sixth cervical vertebra, and opens at the root of the neck into the back part of the innominate vein near its origin, its mouth being guarded by a pair of valves. On the right side, it crosses the first part of the subclavian artery. [WP,unvetted].
Vein which collects blood from the muscles of the neck and drains into the internal jugular.[AAO]
A vessel that drains the chest wall and breats and arises from the superior epigastric vein, accompanies the internal thoracic artery along its course and terminates in the brachiocephalic vein..
Vena comitans of the pericardiacophrenic arteries.
A vein that drains blood from the thymus.
thymic tributary of brachiocephalic vein
The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted].
An unpaired vein which in humans arises from the right ascending lumbar vein or the vena cava, enters the thorax through the aortic orifice in the diaphragm, and terminates in the superior vena cava; unlike humans, mice have a single and left-sided azygos vein that develops from the paired embryonic cardinal venous system and drains most of the right and left thoracic walls into the left anterior vena cava[MP].
check development relationships in different species
A muscle that is part of the pinna and is attached to the auricular cartilage
In some mammals these muscles can adjust the direction of the pinna. In humans these muscles possess very little action. The auricularis anterior draws the auricula forward and upward; the Auricularis superior slightly raises it; and the Auricularis posterior draws it backward.
Auricular muscle attached only to the cartilage of the ear and not to the epicranial aponeurosis
Pharyngeal arch 1 muscle that participates in oral/pharyngeal behaviors, is innervated by masseteric nerve branches of the trigeminal nerve (CN V), and attaches to mandible and zygomatic arch.
The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (...) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati).[well established][VHOG]
The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (...) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati)
The masseter is a jaw muscle of therapsids derived from the m. adductor mandibulae externus, which originates in the adductor chamber (in the temporal fenestra) and inserts on the coronoid process and internal surface of the lower jaw.[Palaeos]
Pharyngeal arch 1 muscle that is innervated by the deep temporal branches of the trigeminal nerve and attaches to the wall of the braincase (including the cranial vault) and mandible.
Pharyngeal arch 1 muscle that is innervated by the deep temporal nerves and attaches to the wall of the braincase and mandible.[FEED]
the superior-most masticatory muscle whose action is closing the jaws; its posterior portion retracts the mandible
The muscle that stabilizes the stapes bone. The stapedius emerges from a pinpoint foramen in the apex of the pyramidal eminence (a hollow, cone-shaped prominence in the posterior wall of the tympanic cavity), and inserts into the neck of the stapes. [WP,unvetted].
The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...).[well established][VHOG]
The larger of the two muscles of the tympanic cavity, is contained in the bony canal above the osseous portion of the auditory tube. Its role is to dampen sounds produced from chewing. It arises from the cartilaginous portion of the auditory tube and the adjoining part of the great wing of the sphenoid, as well as from the osseous canal in which it is contained. Passing backward through the canal, it ends in a slender tendon which enters the tympanic cavity, makes a sharp bend around the extremity of the septum, known as the processus cochleariformis[1], and is inserted into the manubrium of the malleus, near its root[WP].
Skeletal muscle derived from cranial mesoderm and controls eye movements.
todo - resolve discrepancies in which muscles are considered extra-ocular
Any of the six small muscles that control movement of the eyeball within the socket. [TFD][VHOG]
Muscles surrounding the eye (bulbus oculi) and having an effect on eye movements.[AAO]
The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these (extrinsic ocular) muscles tend to be conservative. They change little during the course of evolution.[well established][VHOG]
Mammals have 7 extra-ocular muscles, but humans lack the M. retractor bulbi. Note in ZFA this is the set of muscles.
Myofibers in extraocular muscles are derived from mesoderm, whereas muscle connective tissue cells arise from neural crest.[PMID:16638982]
BTO and MA consider this part of the eye; we follow them here (inferred from skeletal muscle). Not clear if omission from FMA is deliberate.
The medial rectus muscle is a muscle in the orbit. As with most of the muscles of the orbit, it is innervated by the inferior division of the oculomotor nerve (Cranial Nerve III). This muscle shares an origin with several other extrinsic eye muscles, the anulus tendineus, or common tendon. It is the largest of the extraocular muscles and its only action is adduction of the eyeball. [WP,unvetted].
The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution.[well established][VHOG]
Taxon notes (from VHOG): "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.331 [VHOG:0001127]
The lateral rectus muscle is a muscle in the orbit. It is one of six extraocular muscles that control the movements of the eye (abduction in this case) and the only muscle innervated by the abducens nerve, cranial nerve VI. [WP,unvetted].
Cranial nerve VI innervated; lateral in the rectus group.[AAO]
The levator palpebrae superioris (or levator muscle of upper eyelid) is the muscle in the orbit that elevates the superior (upper) eyelid. [WP,unvetted].
The ciliary muscle is a smooth muscle in the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
A sphincter muscle that is part of the iris.
In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]
WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure
The iris dilator muscle (pupil dilator muscle, pupillary dilator, radial muscle of iris, radiating fibers), is a smooth muscle of the eye, running radially in the iris and therefore fit as a dilator. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on α1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina. [WP,unvetted].
A narrow median bridge that joins together the lower thirds of the two lateral (right and left) lobes of the thyroid gland and usually covers the second and the third tracheal rings; the thyroid isthmus is variable in presence and size, can change shape and size, and can encompass a cranially extending pyramid lobe (lobus pyramidalis or processus pyramidalis), remnant of the thyroglossal duct
In mammals and in some reptiles, the thyroid is composed of two lobes connected by an isthmus; in birds and amphibians, the thyroid consists of two isolated lobes. (...) Despite these morphological differences, the ontogeny of the thyroid follows the same pattern in all vertebrates (...).[well established][VHOG]
The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP].
Part of the external carotid which supplies blood to the tongue.[AAO]
relationship loss: part_of external carotid (AAO:0010218)[AAO]
lingual branch of external carotid artery
The Sublingual Artery arises at the anterior margin of the Hyoglossus, and runs forward between the Genioglossus and Mylohyoideus to the sublingual gland. It supplies the gland and gives branches to the Mylohyoideus and neighboring muscles, and to the mucous membrane of the mouth and gums. One branch runs behind the alveolar process of the mandible in the substance of the gum to anastomose with a similar artery from the other side; another pierces the Mylohyoideus and anastomoses with the submental branch of the external maxillary artery. [WP,unvetted].
Part of the external carotid which supplies blood to the tip of the snout where branches go to the tongue and the m. geniohyoideus.[AAO]
The facial artery (external maxillary artery in older texts) is a branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
The occipital artery arises opposite the facial artery, its path is below the posterior belly of digastric to the occipital region. This artery supplies blood to the back of the scalp and sterno-mastoid muscles. Other muscles it supplies are deep muscles in the back and neck. [WP,unvetted].
In human anatomy, the superficial temporal artery is a major artery of the head. It arises from the external carotid artery when it bifurcates into the superficial temporal artery and maxillary artery. Its pulse is palpable superior to the zygomatic arch, anterior and superior to the tragus. [WP,unvetted].
The transverse facial artery is an artery that branches from the superficial temporal artery and runs across the face. [WP,unvetted].
The maxillary artery (or internal maxillary artery in older texts) is an artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
The mental branch of inferior alveolar artery escapes with the nerve at the mental foramen, supplies the chin, and anastomoses with the submental and inferior labial arteries. [WP,unvetted].
mental branch of inferior alveolar artery
ramus mentalis (arteria alveolaris inferior)
The buccal artery (buccinator artery) is small and runs obliquely forward, between the Pterygoideus internus and the insertion of the Temporalis, to the outer surface of the Buccinator, to which it is distributed, anastomosing with branches of the external maxillary and with the infraorbital. [WP,unvetted].
The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic canal. [WP,unvetted].
Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO]
relationship loss: part_of internal carotid (AAO:0010219)[AAO]
The central retinal artery (retinal artery) branches off the ophthalmic artery, running inferior to the optic nerve within its dural sheath to the eyeball. [WP,unvetted].
The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted].
The dorsal nasal artery (nasal artery) is an artery of the head. It is one of the two terminal branches of the ophthalmic artery. [WP,unvetted].
dorsal nasal branch of ophthalmic artery
One of a pair of arteries on the brain that supply oxygen to most medial portions of frontal lobes and superior medial parietal lobes. The 2 anterior cerebral arteries arise from the internal carotid artery and are part of the Circle of Willis.
Coronary artery which emerges from the anterior aortic sinus, between the right auricle and the pulmonary trunk, and supplies the right side of the heart.[FMA]
Coronary artery which emerges from the left posterior aortic sinus, between the left auricle and the pulmonary trunk, and supplies the left side of the heart.[FMA]
The middle cerebral artery (MCA) is one of the three major paired arteries that supplies blood to the cerebrum. The MCA arises from the internal carotid and continues into the lateral sulcus where it then branches and projects to many parts of the lateral cerebral cortex. It also supplies blood to the anterior temporal lobes and the insular cortices. The left and right MCAs rise from trifurcations of the internal carotid arteries and thus are connected to the anterior cerebral arteries and the posterior communicating arteries, which connect to the posterior cerebral arteries. The MCAs are not considered a part of the Circle of Willis. [WP,unvetted].
In human anatomy, the posterior communicating artery is one of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery.
An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO]
todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery
posterior communicating segment of the basilar artery
A small epithelioid structure consisting of a small cluster of chemoreceptive and supporting cells located near the bifurcation of the common carotid artery that serves as a chemoreceptive organ that senses the pH, carbon dioxide, and oxygen concentrations in the blood and plays a crucial role in their homeostatic control.
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior[FMA].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
Lymphatic trunk that connects all tributaries of the thoracic duct tree to the trunk of the left brachiocephalic vein[FMA].
Part of lateral pretrosal artery which supplies blood to the eyelids.[AAO]
relationship loss: part_of lateral pretrosal artery (AAO:0010494)[AAO]
A major artery that supplues the hindbrain and runs along the ventral keel of the hindbrain.
Artery that runs along the ventral keel of the hindbrain. It lies between the primordial hindbrain channels(PHBC). It irrigates the hindbrain and is connected, through the hindbrain, to the PHBC by the central arteries.
The unpaired artery that is formed by the union of the two vertebral arteries, runs forward within the skull just under the pons, divides into the two posterior cerebral arteries, and supplies the pons, cerebellum, posterior part of the cerebrum, and the inner ear[MP].
The major artery supplying the hindbrain, the basilar artery, runs along the ventral keel of the hindbrain in all vertebrates.[well established][VHOG]
The major artery of the midbrain, which crosses the midbrain medially to meet its partner the mesencephalic vein.
Develops from the proximal portion of the primitive mesencephalic artery. Isogai et al. 2001.[TAO]
Develops from the proximal portion of the primitive mesencephalic artery[ZFA:0001068, ZFIN:ZDB-PUB-010205-5].
relationship loss: develops_from primitive mesencephalic artery (TAO:0001062)[TAO]
The superior cerebellar artery (SCA) arises near the termination of the basilar artery. It passes lateralward, immediately below the oculomotor nerve, which separates it from the posterior cerebral artery, winds around the cerebral peduncle, close to the trochlear nerve, and, arriving at the upper surface of the cerebellum, divides into branches which ramify in the pia mater and anastomose with those of the inferior cerebellar arteries. Several branches are given to the pineal body, the anterior medullary velum, and the tela chorioidea of the third ventricle. [WP,unvetted].
The posterior cerebral artery (PCA) is one of a pair of blood vessels that supplies oxygenated blood to the posterior aspect of the brain in human anatomy]. It arises near the intersection of the posterior communicating artery and the basilar artery and connects with the ipsilateral middle cerebral artery (MCA) and internal carotid artery via the posterior communicating artery (PCommA). [WP,unvetted].
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
A portal vein that transports nutrients from the digestive tract to the liver[Kardong].
Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG]
In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]
The celiac artery, also known as the celiac trunk, is the first major branch of the abdominal aorta.
one of the dural venous sinuses and drains the superior sagittal sinus the occipital sinus and the straight sinus, and empties into the sigmoid sinus which in turn reaches the jugular bulb.
groove for right and left transverse sinuses
The superior sagittal sinus (also known as the superior longitudinal sinus), within a human cranium, is an area above/behind the brain, which allows blood veins to span the area, from the top of the head towards the back. It is believed that the cerebrospinal fluid drains through the arachnoid granulations into the dural venous sinuses of the superior sagittal sinus. [WP,unvetted].
Cranial nerve which connects the midbrain to the extra-ocular and intra-ocular muscles.
Somatic efferent fibers which innervate four eye muscles.[AAO]
A cranial nerve that runs to the eye muscles.
Somatic efferent nerve which supplies a single eye muscle, the m. obliquus superior.[AAO]
Homologous trochlear nerves are found in all jawed vertebrates
The human trochlear nerve is derived from the basal plate of the embryonic midbrain.
Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw).
Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]
the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls
Cranial nerve that runs to the eye muscles.
Somatic motor nerve which bifurcates innervating m. rectus lateralis and m. retractor bulbi (eye muscles).[AAO]
Homologous abducens nerves are found in all vertebrates except lampreys and hagfishes.[WP] It controls the movement of a single muscle, the lateral rectus muscle of the eye, in humans. In most other mammals it also innervates the musculus retractor bulbi, which can retract the eye for protection
Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches).
Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO]
Cranial nerve that transmits sound and equilibrium (balance) information from the inner ear to the brain.
Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[AAO]
Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult).
Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO]
Cranial nerve that innervates the muscles of the tongue.
Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis
Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO]
Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]
we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves
The pulmonary arteries carry blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood. In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung. [WP,unvetted].
TODO - add class 'pulmonary artery tree organ'
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
The supraorbital vein begins on the forehead where it communicates with the frontal branch of the superficial temporal vein. It runs downward superficial to the Frontalis muscle, and joins the frontal vein at the medial angle of the orbit to form the angular vein. Previous to its junction with the frontal vein, it sends through the supraorbital notch into the orbit a branch which communicates with the ophthalmic vein; as this vessel passes through the notch, it receives the frontal diploic vein through a foramen at the bottom of the notch. The areas drained by this vessel are the forehead, eyebrow and upper eyelid. [WP,unvetted].
A vein in the chin that is connected to the sublingual and anterior jugular veins and drains into the facial vein.
The retromandibular vein (temporomaxillary vein, posterior facial vein), formed by the union of the superficial temporal and maxillary veins, descends in the substance of the parotid gland, superficial to the external carotid artery but beneath the facial nerve, between the ramus of the mandible and the sternocleidomastoideus muscle. It divides into two branches: an anterior, which passes forward and unites with the anterior facial vein to form the common facial vein. a posterior, which is joined by the posterior auricular vein and becomes the external jugular vein. [WP,unvetted].
The superficial temporal vein is a vein of the side of the head. [WP,unvetted].
The maxillary veins (internal maxillary vein in older sources) consist of a short trunk which accompanies the first part of the internal maxillary artery. It is formed by a confluence of the veins of the pterygoid plexus, and passes backward between the sphenomandibular ligament and the neck of the mandible, and unites with the superficial temporal vein to form the retromandibular vein. [WP,unvetted].
in horses, a branch of the external jugular gives off the occipital and caudal auricular vein
The blood vessels at the vertex and on either side of the head that drain deoxygenated blood into the pterygoid venous plexus.
The anterior auricular veins are veins which drain the anterior aspect of the external ear. [WP,unvetted].
The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted].
The inferior cerebral veins, of small size, drain the under surfaces of the hemispheres. Those on the orbital surface of the frontal lobe join the superior cerebral veins, and through these open into the superior sagittal sinus. Those of the temporal lobe anastomose with the middle cerebral and basal veins, and join the cavernous, sphenoparietal, and superior petrosal sinuses. [WP,unvetted].
The triceps surae is a pair of muscles located at the calf - the gastrocnemius and the soleus. These muscles both insert into the calcaneus, the bone of the heel of the human foot, and form the major part of the muscle of the back part of the lower leg, commonly known as the calf muscle. The triceps surae is connected to the foot through the Achilles tendon, and has 3 heads deriving from the 2 major masses of muscle. The superficial portion (the gastrocnemius) gives off 2 heads attaching to the base of the femur directly above the knee. The deep (profundis) mass of muscle (the soleus) forms the remaining head which attaches to the superior posterior area of the tibia. The triceps surae is innervated by the tibial nerve, specifically, nerve roots L5–S2. [WP,unvetted].
A set of muscles in FMA, a single organ in MA
The Flexor digitorum longus is situated on the tibial side of the leg. At its origin it is thin and pointed, but it gradually increases in size as it descends. This muscle serves to curl the second, third, fourth, and fifth toes (flexion of phalanges II-V). [WP,unvetted].
The Tibialis posterior is the most central of all the leg muscles, and is located in the posterior compartment of the leg. It is the key stabilizing muscle of the lower leg. [WP,unvetted].
Cerebellar veins are veins which drain the cerebellum. More specifically, they are: Superior cerebellar veins Inferior cerebellar veins [WP,unvetted].
The superior cerebellar veins pass partly forward and medialward, across the superior vermis, to end in the straight sinus and the internal cerebral veins, partly lateralward to the transverse and superior petrosal sinuses. [WP,unvetted].
The inferior cerebellar veins are of large size, end in the transverse, superior petrosal, and occipital sinuses. [WP,unvetted].
The central retinal vein (retinal vein) is a short vein that runs through the optic nerve and drains blood from the capillaries of the retina into the larger veins outside the eye. The anatomy of the veins of the orbit of the eye varies between individuals, and in some the central retinal vein drains into the superior ophthalmic vein, and in some it drains directly into the cavernous sinus. [WP,unvetted].
A plexiform vein accompanying the masseteric artery that empty into the pterygoid venous plexus.
A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear.
A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]
the bone at the lower, posterior part of the skull
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended.
part of viscerocranium (facial skeleton) in FMA
the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous
In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process
fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)
The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP].
Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA
A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP]
A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG]
The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG]
todo - homology e.g. mesethmoid of teleost
Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA
the irregularly thin plate that forms part of the medial wall of the orbit behind the frontal process of the maxilla
The infraorbital bone 1 of actinopterygians is homologous with the lacrimal bone (...).[well established][VHOG]
In early lobe-finned fishes and ancestral tetrapods, the lacrimal bone is a relatively large and robust bone, running from the orbit to the nostrils. It forms part of the side of the face, between the nasal bones and the maxilla. In primitive forms, it is often accompanied by a much smaller septomaxilla bone, lying immediately behind the nasal opening, but this is lost in most modern species. The lacrimal bone is often smaller in living vertebrates, and is no longer always directly associated with the nasal opening, although it retains its connection with the orbit. The bone is entirely absent in living amphibians, as well as some reptilian species[ISBN 0-03-910284-X]
One of two small oblong bones, varying in size and form in different individuals; they are placed side by side at the middle and upper part of the face, and form, by their junction, 'the bridge' of the nose[WP]. Paired dermal bones, likened to a bone tube, positioned lateral to the supraethmoid. Nasal bones are transversed by the anterior most part of the supraorbital canals and bear one neuromast foramen in zebrafish[ZFA].
Paired bone of intramembranous origin that roofs the olfactory capsule.[AAO]
Paired dermal bones, likened to a bone tube, positioned lateral to the supraethmoid. Nasal bones are transversed by the anterior most part of the supraorbital canals and bear one neuromast foramen in zebrafish Cubbage and Mabee, 1996.[TAO]
relationship loss: overlaps mesethmoid-nasal joint (TAO:0001677)[TAO]
relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]
Synonym adnasal used in Weitzman 1960, and synonym discussed in Vari 1995.[TAO]
In primitive bony fish and tetrapods, the nasal bones are the most anterior of a set of four paired bones forming the roof of the skull, being followed in sequence by the frontals, the parietals, and the postparietals. Their form in living species is highly variable, depending on the shape of the head, but they generally form the roof of the snout or beak, running from the nostrils to a position short of the orbits. In most animals, they are generally therefore proportionally larger than in humans or great apes, because of the shortened faces of the latter. Turtles, unusually, lack nasal bones, with the prefrontal bones of the orbit reaching all the way to the nostrils (ISBN 0-03-910284-X)
A paired dermal bone situated in the mid-palate[Palaeos].
Dermal bone that forms the antero-lateral region of the palate and is located ventral to the autopalatine. The dermopalatine is bilaterally paired and usually bears teeth.[TAO]
Dermopalatine: same as palatine. The prefix is used by fish people because the palatine is a dermal replacement bone for a section of the autopalatine section of the palatoquadrate. In that context, palatine is potentially ambiguous.[Palaeos]
In ostariophysans, the dermopalatine is absent.[TAO]
the quadrilateral bone that forms the prominence of the cheek
The jugal is a skull bone found in most reptiles, amphibians, and birds. In mammals, the jugal is often called the malar or Zygomatic. It is connected to the quadratojugal and maxilla, as well as other bones, which may vary by species. This bone is considered key in the determination of general traits of the skull, in the case of creatures, as with dinosaurs in paleontology, whose entire skull has not been found[Wikipedia:Jugal_bone].
The zygomatic bone is a paired dermal bone which articulates with the maxilla. In humans it also articulates with the temporal bone, the sphenoid bone and the frontal bone. The zygomatic is homologous to the jugal bone of other tetrapods. It is situated at the upper and lateral part of the face and forms the prominence of the cheek, part of the lateral wall and floor of the orbit, and parts of the temporal and infratemporal fossae. It presents a malar and a temporal surface; four processes, the frontosphenoidal, orbital, maxillary, and temporal; and four borders[WP,modified][Wikipedia:Zygomatic_bone].
(...) and the infraorbital bone 3 of advanced actinopterygians (is homologous) with the jugal bone of sarcopterygians.[well established][VHOG]
In humans it also articulates with the temporal bone, the sphenoid bone and the frontal bone. The zygomatic is homologous to the jugal bone of other tetrapods. It is situated at the upper and lateral part of the face and forms the prominence of the cheek, part of the lateral wall and floor of the orbit, and parts of the temporal and infratemporal fossae. It presents a malar and a temporal surface; four processes, the frontosphenoidal, orbital, maxillary, and temporal; and four borders [Wikipedia:Zygomatic_bone, http://en.wikipedia.org/wiki/Jugal_bone]
vHOG says is homologous to infraorbital 3.
A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton.
consider merging with dentary - for now we make it a mammal-specific subclass.
Note in ZFA 'mandible' is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term 'mandibular symphysis' refers to the dentary
'mandible' also refers to either the upper OR lower part of the beak in birds
A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified].
Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]
relationship loss: part_of hyoid plate (AAO:0000664)[AAO]
The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia.
One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted].
This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5.
The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG]
Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG]
Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry.
The stapes or stirrup is the stirrup-shaped small bone or ossicle in the middle ear which is attached to the incus laterally and to the fenestra ovalis, the 'oval window' medially. The oval window is adjacent to the vestibule of the inner ear. The stapes is the smallest and lightest bone in the human body. The stapes transmits the sound vibrations from the incus to the membrane of the inner ear inside the fenestra ovalis. The stapes is also stabilized by the stapedius muscle, which is innervated by the facial nerve. In non-mammalian vertebrates, the bone homologous to the stapes is usually called the columella; however, in reptiles, either term may be used[WP,unvetted].
This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG]
'This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.' Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357?[VHOG].
As the stapes first develops embryologically from the 6th to 8th week of life, it surrounds the stapedial artery, which supplies the majority of the vasculature of the embryonic head. After that period, the external carotid artery is generated and takes over for the stapedial artery, which subsequently involutes, leaving the stapes with a windowframe-like structure[WP] The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert's cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes.
The incus or anvil is the anvil-shaped small bone or ossicle in the middle ear. It connects the malleus to the stapes. It was first described by Alessandro Achillin of Bologna. The incus transmits sound vibrations from the malleus to the stapes. The incus only exists in mammals, and is derived from a reptilian upper jaw bone, the quadrate bone. Embryologically it is derived from the first pharyngeal arch along with the rest of the bones of mastication, such as the maxilla and mandible. [WP,unvetted].
According to this theory (Reichert-Gaupp theory), the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...).[well established][VHOG]
The malleus or hammer is a hammer-shaped small bone or ossicle of the middle ear which connects with the incus and is attached to the inner surface of the eardrum. The word is Latin for hammer. It transmits the sound vibrations from the eardrum to the incus. The malleus is unique to mammals, and evolved from a lower jaw bone in basal amniotes called the articular, which still forms part of the jaw joint in reptiles. Embryologically it is derived from the first pharyngeal arch along with the rest of the bones of mastication, such as the maxilla and mandible. [WP,unvetted].
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
The organ of hearing and of equilibrium. [TFD][VHOG]
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
Part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO].
The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]
One of the bones of the occiput, the part of the skull which articulates with the spine. The basioccipital is located (if present) ventral to the foramen magnum. It often rests on or articulates with the basisphenoid, as well as meeting the exoccipitals. The basioccipital usually forms most (sometimes all) of the occipital condyle(s) and the ventral margin of the foramen magnum.
An unpaired medial bone contributing to the ventral margin of the foramen magnum that extends into the floor of the brain cavity. It can contribute to the centromedial portion of the occipital condyle.[AAO]
Chondral bone that articulates with the exoccipitals dorsally, the prootics anteriorly, the parasphenoid ventrally, and the first free vertebra posteriorly. The basioccipital forms the floor of the foramen magnum. The basioccipital is an unpaired medial bone.[TAO]
relationship loss: overlaps basioccipital-exoccipital joint (TAO:0002038)[TAO]
relationship loss: overlaps parasphenoid-basioccipital joint (TAO:0001832)[TAO]
relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]
In some teleosts the anterior vertebral centra fuse to the basioccipital forming a monopartite occipital condyle.[TAO]
Paired cartilage bone that bears a large foramen (lateral occipital foramen). Contacts the supraoccipital dorsally, the epiotic laterally and the basioccipital ventrally. Forms the posterior hind margin of the cranium and borders the lateral and posterior margins of the forum (foramen) magnum.
TODO - check FMA - currently we place this as both of a zone of bone organ and an (endochondral) bone. Removed endochondral bone classification for now, violates disjointness axiom
Endochondral bone that articulates with the epiotic dorsally, the pterotic and intercalar laterally and the basioccipital medio-ventrally. The exoccipitals form the lateral borders of the foramen magnum and houses the foramina for the passage of the vagus and glossopharyngeal nerves, X and IX respectively. The exoccipital is a paired bone.[TAO]
Endochondral bone that forms the posterior end of the neurocranium and the margin of the foramen magnum. In addition, this bone forms either part of or all or the occipital condyle.[AAO]
relationship loss: develops_from occipital arch cartilage (TAO:0001504)[TAO]
relationship loss: overlaps prootic-exoccipital joint (TAO:0002034)[TAO]
In some teleosts the exoccipital dorsally contacts the supraoccipital directly or through connective tissue.[TAO]
The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted].
The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG]
A bone which is fused with the temporal bone in many mammals and forms part of the cheek region articulating with quadrate and pterygoid in other vertebrates.
consider separate class for squamosal OR making squamosal the primary label
Paired, intramembranous bones that lie at the posterolateral margins of the skull. Lateral and dorsal to the quadrate.[AAO]
The squamosal bone is part of the dermatocranium in early tetrapods and becomes part of the mammalian occipital and temporal bones. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.246, see_Liem_KF][VHOG]
The squamosal bone, which is homologous with the squama, and forms the side of the cranium in many bony fish and tetrapods. Primitively, it is a flattened plate-like bone, but in many animals it is narrower in form, for example, where it forms the boundary between the two temporal fenestrae of diapsid reptiles
Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball.
Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO]
in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit
one of the larger of the several holes at the base of the skull that transmit nerves through the skull. The foramen ovale is situated in the anterior part of the sphenoid bone, posteriolateral to the foramen rotundum..
An aperture in the great wing of the sphenoid for vessels and nerves. [TFD][VHOG]
The nervus intermedius, or intermediate nerve, is the part of the facial nerve (cranial nerve VII) located between the motor component of the facial nerve and the vestibulocochlear nerve (cranial nerve VIII). It contains the sensory and parasympathetic fibers of the facial nerve. Upon reaching the facial canal, it joins with the motor root of the facial nerve at the geniculate ganglion. [WP,unvetted].
sensory component of the VIIth (facial) nerve
the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve)
resolve facial VII vs geniculate (see EHDAA2)
These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]
The group of neuron cell bodies associated with the ninth cranial nerve.
An eyelash or simply lash is one of the hairs that grow at the edge of the eyelid. Eyelashes protect the eye from debris and perform some of the same function as whiskers do on a cat or a mouse in the sense that they are sensitive to being touched, thus providing a warning that an object is near the eye (which is then closed reflexively). The greek word for eyelash is 'blepharis'. This word is often used as a root in biological terms
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
this class was made obsolete as it conflated the facial skeleton with the splanchnocranium. The facial skeleton includes: * Inferior nasal concha * Lacrimal bone * Mandible * Maxilla * Nasal bone * Palatine bone * Vomer * Zygomatic bone. The hyoid is sometimes included, and sometimes excluded (FMA includes it) (See also notes for ethmoid bone). The splanchoncranium is the endoskeleton derived from pharyngeal arches.
A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
TODO - check claw vs nail. A primate's nail consists of the unguis alone; the subunguis has disappeared.
The nasal septum separates the left and right airways in the nose, dividing the two nostrils. It is depressed by the Depressor septi nasi muscle. [WP,unvetted].
We follow AAO in making this part of the nasal skeleton
A median dividing wall, sagittally directed, which divides the nasal cavity into the right and the left nasal fossae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Medial vertical wall between nasal capsules.[AAO]
Medial, vertical plate that separates the nasal capsules.[AAO]
Whatever the common ancestor of the lamprey and gnathostomes may have looked like, it most likely possessed a neural-crest-derived premandibular ectomesenchyme closely associated with the NHP. Invention of the jaw subsequently required a space for the nasal septum and maxillary process to develop, which might have been provided by subdivision of the NHP into the nasal placode and the hypophysis (diplorhiny, the state of bilaterally separated nasal openings, would also have been a prerequisite for this).[well established][VHOG]
An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
defne the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.
Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]
a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity].
Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]
in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
See notes for jaw w.r.t skeletal element vs subdivision of head.
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane
In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva.
FMA divides this into skin, fascia, conjunctiva
A tetrapod's eye usually has one or more eyelids that can move across its surface and protect and cleanse it. The eye of lissamphibians has a stationary upper eyelid but a movable and transparent lower one.[well established][VHOG]
the groups of nerve cell bodies associated with the twelve cranial nerves
Ganglion which is located in the head.[TAO]
cranial ganglion part of peripheral nervous system
Nuclear complex containing subnuclei that give rise to the axons of the occulomotor nerve, both motor and parasympathetic fibers, situated at the midline at the level of the superior colliculus in the midbrain tegmentum (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 533-534).
The nucleus of the oculomotor nerve (cranial nerve III)[XAO:0004389].
The part of the palate formed from the fusion of the two palatine shelves, extensions of the maxillary prominences.
present in mammals and some reptiles. A similar structure is found in crocodilians, but, in most other tetrapods, the oral and nasal cavities are not truly separate. The secondary palate is formed by bilateral medial extensions of maxillary processes. The extensions (palatine processes) meet at the midline, merging dorsally with nasal septum and rostrally with primary palate. The secondary palate (hard palate) separates nasal and oral cavities. Caudal extension of the secondary palate into the pharynx, forms a soft palate which divides the rostral pharynx into dorsal (nasopharynx) and ventral (oropharynx) chamber.
Nucleus extending from the upper spinal cord through the pontine tegmentum that receives sensory inputs from the trigeminal nerve. It is continuous caudally with the dorsal gray matter of the spinal cord.
Elongated nucleus located in the midbrain tegmentum that receives proprioceptive input from both teh extraocular and the masticatory muscles. Contrary to the general rule, the cell bodies that give rise to these sensory fibers are located within the mesencephalic nucleus rather than in a peripheral ganglion. Some of the sensory fibers in the mesencephalic root give off collaterals to the trigeminal motor nucleus, thereby providing the anatomic basis for the monosynaptic jaw reflex. (Heimer, L. The Human Brain and Spinal Cord, 2nd ed. 1996, page 248).
develops from NC in some species[UBERONREF:0000002] Not of NC origin[doi:10.1002/dvdy.1197].
part of midbrain tegmentum in NIF and MA. the neurons of the mesencephalic trigeminal nucleus are the only centrally located primary sensory neurons in amniotes; all others are extramedullary
mesencephalic nucleus of the trigeminal nerve
nucleus mesencephalicus nervi trigeminalis
nucleus tractus mesencephalici nervi trigemini
nucleus tractus mesencephalicus nervi trigemini
mesencephalic nucleus of trigeminal nerve
The nucleus ambiguus (literally 'ambiguous nucleus') is a region of histologically disparate cells located just dorsal to the inferior olivary nucleus in the lateral portion of the upper medulla. It receives upper motor neuron innervation directly via the corticobulbar tract This nucleus gives rise to the efferent motor fibers of the vagus nerve terminating in the laryngeal and pharyngeal muscles, as well as to the efferent motor fibers of the glossopharyngeal nerve (CN IX) terminating in the stylopharyngeus. [WP,unvetted].
Any of the nuclei of the cochlear nuclear complex.
cochlear nucleus of eighth cranial nerve
The inferior vestibular nucleus is the vestibular nucleus which lies near the fourth ventricle. [WP,unvetted].
The medial vestibular nucleus is one of the vestibular nuclei. It is located in the medulla oblongata. Lateral vestibulo-spinal tract (lateral vestibular nucleus 'Deiters')- via ventrolateral medulla and spinal cord to ventral funiculus (lumbo-sacral segments). Ipsilaterally for posture Medial vestibulo-spinal tract (medial, lateral, inferior, vestibular nuclei), bilateral projection via descending medial longitudinal fasciculus to cervical segments. DESCENDING MLF. Bilaterally for head/neck/eye movements [WP,unvetted].
A muscular organ in the floor of the mouth.
in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.
A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]
Muscular organ in the floor of the mouth.[FEED]
The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586].
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods
The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions
One of the paired paranasal sinuses, located in the body of the sphenoid bone and communicating with the highest meatus of the nasal cavity on the same side[MESH]. The sphenoidal sinuses (or sphenoid) contained within the body of the sphenoid vary in size and shape; owing to the lateral displacement of the intervening septum they are rarely symmetrical. The following are their average measurements: vertical height, 2.2 cm. ; transverse breadth, 2 cm. ; antero-posterior depth, 2.2 cm. [WP,unvetted].
The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis.
A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. Taste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx.
One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG]
Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG]
arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN10:1607950324 (todo - request cell terms from CL)
the section of the pharynx that lies above the soft palate
The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG]
In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane
the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis
One of the three anatomic divisions of the pharynx that lies posterior to the mouth and is continuous above with the nasopharynx and below with the laryngopharynx. It extends behind the mouth from the soft palate above to the level of the hyoid bone below and contains the palatine and lingual tonsils. [TFD][VHOG]
A anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
the lymph tissue in the roof and posterior wall of the nasopharynx
soft tissue constituting the back of the roof of the mouth. The soft palate is distinguished from the hard palate at the front of the mouth in that it does not contain bone[WP]. The soft palate is the posterior portion of the palate extending from the posterior edge of the hard palate[GO].
A muscular arch-shaped structure [is this an 'anatomical cluster�?] that is composed of the musculus uvuli and parts of tensor veli palatini, levator veli palatini, palatoglossus and palatopharyngeus and attaches to the hard palate and modulates the connections between the oral cavity and pharynx soft tissue arch .[FEED]
Conic projection from the posterior edge of the middle of the soft palate, composed of connective tissue containing a number of racemose glands, and some muscular fibers.
In a study of eight mammals a small underdeveloped uvula was found only in baboons
the circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils
Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible.
Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG]
The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG]
In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted]
in mice, submandibular gland development initiates as a thickening of the oral epithelium; around E12 an initial (single) epithelial bud on a stalk grows into a condensing neural crest-derived mesenchyme; clefts in the epithelium result in 3-5 epithelial buds at E13.5, and branching morphogenesis occurs with continued proliferation, successive rounds of cleft formation, duct elongation, and duct lumen formation, so that by E14 the gland is highly branched (multi-lobed); functional differentiation, with the appearance of proacinar cells and secretory products begins after E15 and continues to birth; acinar differentiation continues postnatally with final differentiation of the granular convoluted tubules at puberty[MGI:anna]
The submandibular is the first major salivary gland to develop in the embryo, followed by the neighbouring sublingual and then the parotid.[PMID:17336109]
Heterogeneous cluster that connects the pharynx to the tracheobronchial tree[FMA].
An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]
Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]
(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]
The largest cartilage of the larynx, having two broad processes that join anteriorly to form the Adam's apple. [TFD][VHOG]
[In anura] a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) [In mammals] Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]
The cartilaginous structures that support the larynx.
the paired triangular laryngeal cartilages located postlaterally at the level of the thyroid cartilage
Paired, anteroposteriorly elongated cartilages that are associated with the vocal cords. These cartilages are medially separated and hemispherical, and their concave side faces ventromedially.[AAO]
The corniculate cartilages (cartilages of Santorini) are two small conical nodules consisting of yellow elastic cartilage, which articulate with the summits of the arytenoid cartilages and serve to prolong them posteriorly and medially. They are situated in the posterior parts of the aryepiglottic folds of mucous membrane, and are sometimes fused with the arytenoid cartilages. [WP,unvetted].
The most superior of the laryngeal cartilages, which is found at the root of the tongue and folds back over the entrance to the larynx during swallowing.
A ligament that is part of a larynx and connexts the cartilages of the larynx
Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP].
A lymphoid follicle that contains a germinal center.
A parenchyma that is part of a thyroid follicle [Automatically generated definition].
A capsule that surrounds a parathyroid gland.
A parenchyma that is part of a parathyroid gland [Automatically generated definition].
A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta.
TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal
this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye
Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular.
Mineralized collagen containing substance that forms the tooth structure.[TAO]
Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG]
Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]. Editors note: note the asserted dual is_a parentage, as dentine is both skeletal tissue and a substance
A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP].
current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)
Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]
Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.
Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO]
Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA:55630].
Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W]
The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP].
Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO]
The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG]
A segment in the hyoidean arch between the epihyal and tympanohyal[biology-online]. The interhyal is a small rod-like element that connects the ventral and dorsal parts of the hyoid arch. It articulates laterally with the posterior end of the epihyal and medially at the cartilaginous junction between the hyomandibula and the symplectic. It remains cartilaginous in adult zebrafish and other cypriniforms[ZFA].
distal part of styloid process of temporal bone
The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO].
The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]
Visible part of the ear that resides outside of the head. The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch). The filtering effect of the human pinna preferentially selects sounds in the frequency range of human speech. In various species, the pinna can also signal mood and radiate heat.
The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG]
The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO].
FMA treats periodontium and periodontal ligament as the same
Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart).
Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO]
The frontal sinus occupies the dorsal part of the skull medial to the orbit. It overlaps cranial and nasal cavities and is often referred to as the conchofrontal sinus. .
A unique feature in the horse is that the frontal sinus communicates with the caudal maxillary sinus via the frontomaxillary opening
A thickened and indented region in the midline in the floor of the rostral part of the pharyngeal region of the foregut, located between the second and third branchial arches that is the first indication of the thyroid primordium. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.132]
the small curved bones that extends horizontally along the lateral wall of the nasal passage
In humans, the turbinates divide the nasal airway into three groove-like air passages –and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue.
Turbinals are only ossified in birds and derived synapsids.
FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here
Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina[ZFA]. The dental papilla is a condensation of ectomesenchymal cells called odontoblasts, seen in histologic sections of a developing tooth. It lies below a cellular aggregation known as the enamel organ. The dental papilla appears after 8-10 weeks intra uteral life. The dental papilla gives rise to the dentin and pulp of a tooth. The enamel organ, dental papilla, and dental follicle together forms one unit, called the tooth germ. This is of importance because all the tissues of a tooth and its supporting structures form from these distinct cellular aggregations.
Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]
Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]
Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG]
One of the paired paranasal sinuses, located in the body of the maxilla, communicating with the middle meatus of the nasal cavity.
Epithelial tube that transports milk[GO].
the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
the ring-like space, filled with aqueous humor, between the iris/pupil anteriorly and the lens and ciliary body posteriorly
The posterior chamber should not be confused with vitreous chamber.
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [doi:dx.doi.org/10.1006/dbio.1998.9019]
The lacrimal canaliculi, also known as the lacrimal canals or lacrimal ducts, are the small channels in each eyelid that commence at minute orifices, termed puncta lacrimalia, on the summits of the papillae lacrimales, seen on the margins of the lids at the lateral extremity of the lacus lacrimalis. The superior duct, the smaller and shorter of the two, at first ascends, and then bends at an acute angle, and passes medialward and downward to the lacrimal sac. The inferior duct at first descends, and then runs almost horizontally to the lacrimal sac. At the angles they are dilated into ampullæ. Microscopically, they are lined by nonkeratinizing stratified squamous epithelium surrounded by fibrous tissue. Outside the latter is a layer of striped muscle, continuous with the lacrimal part of the Orbicularis oculi; at the base of each lacrimal papilla the muscular fibers are circularly arranged and form a kind of sphincter. [WP,unvetted].
TODO - resolve lacrimal canaliculus vs larcimal duct
the central circular aperture of the iris through which light rays enter the eye
The circular orifice in the centre of the iris, through which light enters into the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
the smooth stratified squamous epithelium that covers the outer surface of the cornea
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709].
Disease notes: implicated in rheumatoid arthritis.
A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
MP treats posterior uvea and optic choroid as distinct
the lamellated connective tissue of the cornea between the Bowman and Descemet membranes
Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]
A double layer covering the ciliary body that produces aqueous humor.
The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae.
the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]
Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]
Any of the layers that make up the retina[MP].
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP].
A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]
The monolayer of pigmented epithelium covering the neural retina.[AAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
The optic disc or optic nerve head is the location where ganglion cell axons exit the eye to form the optic nerve. There are no light sensitive rods or cones to respond to a light stimulus at this point. This causes a break in the visual field called 'the blind spot' or the 'physiological blind spot'. The optic nerve head in a normal human eye carries from 1 to 1.2 million neurons from the eye towards the brain. [WP,unvetted].
The small blind spot on the surface of the retina. It is the point where the fibers of the retina leave the eye and become part of the optic nerve. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod (reference 2).[well established][VHOG]
Obsoleted as it accidentally grouped macula and macula lutea
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
A depression in the inner retinal surface within the macula lutea, the photoreceptor layer of which is entirely cones and which is specialized for maximum visual acuity
A small pit in the center of the macula lutea, the area of clearest vision, where the retinal layers are spread aside, and light falls directly on the cones. [TFD][VHOG]
Definition of fovea centralis should be considered here as 'an area centralis at the visual axis' (reference 1). There is an uncertaincy of the relation, because: 1.-The fovea first appeared in evolution in the temporal retina of fishes. Then, in birds, the nasal fovea and bifoveal system with nasal and temporal foveas developed. The fovea disappeared in primitive mammals, and reappeared in primates. A residue of the fovea is conserved in the visual streak, and the disappearance and reappearance of the fovea, in primitive mammals and primates respectively, correlates with degeneration and restoration of cone pigment genes in photoreceptors (reference 2). 2.-Many retinal features (foveas, trichromacy, midget pathways and associated cell types) appear specific to primates. This has led to investigations in parallel with other mammalian models such as cat or rabbit. Correlation of the results often proves to be difficult, since an evolutionary scenario with transitions between the mammalian models is largely lacking (reference 3).[uncertain][VHOG]
The fovea is also a pit in the surface of the retinas of many types of fish, reptiles, and birds. Among mammals, it is found only in simian primates. The retinal fovea takes slightly different forms in different types of animals. For example, in primates, cone photoreceptors line the base of the foveal pit, the cells that elsewhere in the retina form more superficial layers having been displaced away from the foveal region during late fetal and early postnatal life. Other foveae may show only a reduced thickness in the inner cell layers, rather than an almost complete absence
The layer within the retina where the photoreceptor cell receptor segments reside.
we follow MA and ZFA in subdividing this into inner and outer segments
stratum segmentorum externorum et internorum (retina)
The row of jucntional complexes between the plasma membranes of rod segments and the Muller glia cells; this barrier separates the layer of inner and outer segments of the rods and cones from the outer nuclear layer and forms a blood-retina barrier[MP].
The layer within the retina where the photoreceptor cell bodies reside.
The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO].
The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]
Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia).
The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176].
AO notes http://uri.neuinfo.org/nif/nifstd/nlx_anat_1005031 appears to be retired
Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer
a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer].
NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]
Fiber layer adjacent the retinal ganglion cell layer which is comprised of their axons as they traverse to the optic nerve[ZFA]. The retinal nerve fiber layer (nerve fiber layer, stratum opticum, RNFL) is formed by the expansion of the fibers of the optic nerve; it is thickest near the porus opticus, gradually diminishing toward the ora serrata. As the nerve fibers pass through the lamina cribrosa sclerae they lose their medullary sheaths and are continued onward through the choroid and retina as simple axis-cylinders. When they reach the internal surface of the retina they radiate from their point of entrance over this surface grouped in bundles, and in many places arranged in plexuses. Most of the fibers are centripetal, and are the direct continuations of the axis-cylinder processes of the cells of the ganglionic layer, but a few of them are centrifugal and ramify in the inner plexiform and inner nuclear layers, where they end in enlarged extremities.
The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP].
Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3].
Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia)
The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842].
The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]
http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired
Body substance in liquid state contained in the anterior and posterior chambers of the eyeball[FMA]. The aqueous humour is a thick watery substance filling the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
Body substance of semisolid state which constitutes the vitreous body of the eye.[FMA]
FMA distinguishes between a portion and the whole portion. We equate with whole portion here, but this is arbitrary
Mucoid tissue in the vitreous chamber of the eyeball. Examples: There are only two instances, right and left vitreous bodies.[FMA]
in many AOs these are exact synonyms, but FMA has a part of link between portion of vitreous humor and this
The posterior chamber is a narrow chink behind the peripheral part of the iris of the eye, and in front of the suspensory ligament of the lens and the ciliary processes the Posterior Chamber consists of small space directly posterior of the iris but anterior to the lens. [WP,unvetted].
The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells.
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
The cells of the lens epithelium regulate most of the homeostatic functions of the lens.[6] As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
the elastic, clear, membrane-like structure, that is outer most layer of the lens
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens, http://en.wikipedia.org/wiki/Lens_(anatomy)#Lens_capsule]
ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia
ganglion of sympathetic part of autonomic division of nervous system
sympathetic part of autonomic division of nervous system ganglion
Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord.
Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands.
Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA].
in FMA this is a subtype of junction rather than tissue
the mucous membrane that lines the inner surface of the eyelids and the front of the eyeball
The part of the conjunctiva, a thin transparent mucous membrane, that covers the posterior surface of the eyelids.
A nerve plexus that is part of a somatic nervous system [Automatically generated definition].
The brachial plexus is an arrangement of nerve fibers, running from the spine, formed by the ventral rami of the lower cervical and upper thoracic nerve root, specifically from below the fifth cervical vertebra to above the first thoracic vertebra. It proceeds through the neck, the axilla (armpit region) and into the arm. [WP,unvetted].
check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus'
A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG]
To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]
The anterior divisions of the lumbar nerve, sacral nerve, and coccygeal nerves form the lumbosacral plexus, the first lumbar nerve being frequently joined by a branch from the twelfth thoracic. For descriptive purposes this plexus is usually divided into three parts: lumbar plexus sacral plexus pudendal plexus [WP,unvetted].
A nerve plexus that is part of an autonomic nervous system [Automatically generated definition].
The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP].
Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands.
The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland].
In humans, they are situated in the upper, outer portion of each orbit
Innervation is highly complex and species-specific
A modified lobulated sebaceous gland at the rim of an eyelid, responsible for the supply of meibum.
in mice, meibomian gland development is initiated around E18.5 with the formation of an epithelial placode and mesenchymal condensation, similar to that observed in hair follicle development; invagination of the epithelium into the developing mesenchyme then continues from birth to about P3 with initial branching of the epithelial cord detected at P5; by P8 the developing meibomian gland shows extensive ductal branching and the formation of distinct acini with mature meibomian glands present by P15 or eyelid opening[PMID:20664693]
Orifice separating upper and lower eyelids. In the human adult this measures about 10mm vertically and 30 mm horizontally. It can be reduced in size in fetal alcohol syndrome. In Trisomy 9 the palpebral fissures can be upslanting. [WP,modified].
any of the coil glands of the skin that secrete sweat
TODO - check if all sweat glands are epidermal - see EMAPA:29743
A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG]
Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG]
In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation
A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP].
sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass.
Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]
Sebaceous glands are also limited to mammals.[well established][VHOG]
A membranous sheet that acts as the anterior boundary of the orbit. It extends from the orbital rims to the eyelids[WP].
One of the cartilage structures in the nose that provide form and support[WP].
The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx.
the paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity
Arise as epithelial lined diverticula of the lining of the nasal cavity. The extent of sinus development varies with species, most of the development occurs postnatally
The mucous membrane that lines the nasal cavity[MP].
TODO - check lining vs part of. split olfactory and nasal mucosa?
Aqueous substance secreted by the lacrimal gland.
The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001].
FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton.
One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands.
There are 3 pairs of major salivary glands in human and mouse
One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
There are over 600 minor salivary glands located throughout the oral cavity within the lamina propria of the oral mucosa. They are 1-2mm in diameter and unlike the other glands, they are not encapsulated by connective tissue only surrounded by it. The gland is usually a number of acini connected in a tiny lobule. A minor salivary gland may have a common excretory duct with another gland, or may have its own excretory duct. Their secretion is mainly mucous in nature (except for Von Ebner's glands) and have many functions such as coating the oral cavity with saliva[WP].
The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted].
A mammalian salivary gland located caudal to the ear. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-22, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The mouse parotid, exorbital lacrimal gland and exocrine pancreas have similar histological appearances[ISBN10:0123813611]
the small mucin-producing salivary glands in the floor of the mouth beneath the tongue, anterior to the submandibular gland
One of a pair of small salivary glands situated under the mucous membrane of the floor of the mouth, beneath the tongue. [TFD][VHOG]
Most mammals have well-developed parotid, mandibular, and sublingual glands.[well established][VHOG]
Single lobed in mouse; largest acini of the 3 rodent salivary glands. In human and mouse, secretions are predominantly mucinous
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
Lip that covers the upper portion of the mouth.[TAO].
Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG]
Lip that covers the lower portion of the mouth.[TAO].
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin
A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted].
Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved.
One of three half-circular, interconnected tubes located inside each ear[WP].
Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]
In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG]
MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal
One of three fluid-filled toroidal spaces, arranged orthogonally to each other in each ear, that detect angular acceleration. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]
relationship loss: develops_from anterior semicircular canal primordium (TAO:0000469)[TAO]
relationship loss: develops_from posterior semicircular canal primordium (TAO:0000412)[TAO]
relationship loss: develops_from lateral semicircular canal primordium (TAO:0000232)[TAO]
the spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified].
A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG]
Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG]
The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)'
the cochlea is coiled in most mammals, monotremes being the exceptions.
sources vary in connection to bony labyrinth
Transudate contained in the osseous labyrinth outside the membranous labyrinth.[FMA]
Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation.
The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]
The soft lower part of the external ear, projecting below the antitragus.
The earlobe is composed of tough areolar and adipose (fatty) connective tissues, lacking the firmness and elasticity of the rest of the pinna. Since the earlobe does not contain cartilage the earlobe has a large blood supply and may help to warm the ears and maintain balance but generally earlobes are not considered to have any major biological function.
cartilage of the pinna and much of the external ear canal.
Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP]
A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG]
inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now
A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct.
chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104]
this class is used more generically than in FMA, and includes e.g. cortex of hair
Transudate contained within the membranous labyrinth.[FMA]
the larger of the two otolith organs in the vestibule
The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]
XAO/AAO to be checked - see https://github.com/seger/aao/issues/5; AAO has both utricle and utriculus; these are generally considered synonyms - e.g. http://www.fishbase.org/glossary/Glossary.php?q=utriculus
the smaller of the two otolith organs in the vestibule
The most ventral chamber of the membranous labyrinth. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG]
XAO/AAO to be checked - see https://github.com/seger/aao/issues/5
An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP].
TODO - check cochlear duct vs cochlear aqueduct vs scala media
The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG]
In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG]
Any of the three loop-shaped membranous inner tubular parts of the semicircular canals that are about one-fourth the diameter of the corresponding outer bony canals, that communicate at each end with the utricle, and that have near one end an expanded ampulla containing an area of sensory epithelium
TODO - check canal vs duct. see http://en.wikipedia.org/wiki/File:Gray927.png
In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG]
Vertebrata is characterized by three synapomorphies. (...) Vertebrates also have at least two vertical semicircular ducts (...). In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]
Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution. [ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.58] ; In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]
the small membranous canal, connecting with both saccule and utricle of the membranous labyrinth, passing through the aqueduct of vestibule, and terminating in the endolymphatic sac
Duct that is part of the inner ear and connects to the semicircular canals ending in a pouch.[TAO]
The canalis reuniens of Hansen is part of the human inner ear. It connects the lower part of the saccule to the ductus cochlearis near its vestibular extremity.
The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals.
the division of the spiral canal of the cochlea lying on the apical side of the spiral lamina and vestibular membrane
the division of the spiral canal of the cochlea lying on the basal side of the spiral lamina
cartilaginous part of external acoustic meatus
external acoustic meatus cartilaginous part
Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP].
The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans.
A cartilage that is part of a external ear [Automatically generated definition].
A zone of skin that is part of a chest [Automatically generated definition].
anterolateral part of thorax zone of skin
zone of skin of anterior thoracic region
zone of skin of anterolateral part of thorax
One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]
Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]
The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]
Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally.
Lower lateral part of the cerebral hemisphere. (MSH)
Boundary notes: It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. [Wikipedia:Temporal_lobe]
Upper central part of the cerebral hemisphere. (MSH)
Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.
Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent[FMA:61833].
Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion.
check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)
Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease[Wikipedia:Putamen].
All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]
Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle.
Nucleus of brain which is located medially to the putamen and laterally to the internal capsule[FMA][FMA:61835].
BTO and MA are inconsistent w.r.t striatum and pallidum being non-overlapping as in ABA. Note that we have pallidum as part_of basal gangion, so we can make the direct link to basal ganglion. ISBN10:1588900649 says: ... a derivative of the diencephalon, seperates as a result of growing fibers of theinternal capsule and is finally displaced into telencephalon. only a small medial remnannt remains, the entopeduncular nucleus. The globus pallidus should be regarded as part of the subthalamus
Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM).
Subdivision of basal ganglion of telencephalon which is an almond-shaped gray mass in the dorsomedial part of the temporal lobe[FMA:61841]
One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei.[well established][VHOG]
MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype
Cells lying generally in front of Regional_part_of_septal_nuclei, lying ventral to and slightly medial to the lateral septal nucleus. Neurons in this nucleus give rise to the bulk of efferents from the septal nuclei. A major projection from the medial septal nucleus terminates in the hippocampal formation (Adapted from Brodal, 1981).
A nucleus in the septal area, coextensive with the diagonal band of Broca; it has afferent and cholinergic efferent connections with a variety of forebrain and brain stem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdaloid bodies.
The medial septal nucleus is one of the septal nuclei. It plays a role in the generation of theta waves[Wikipedia:Medial_septal_nucleus].
A brain structure that is part of the septal nuclear complex. It is connected with the hippocampus, hypothalamus and amygdala.
nuclei of horizontal and vertical limbs of diagonal band
A brain structure in the forebrain wrapped around the stria terminalis. It's largest extent can be found around the crossing of the anterior commissure[INCF].
interstitial nucleus of stria terminalis
nucleus interstitialis striae terminalis
nucleus proprius stria terminalis (bed nucleus)
One of the seven small groups of granule cells in the polymorph layer of the olfactory tubercle and one large group, the insula magna, which lies along the border between septum, nucleus accumbens and nucleus of the diagonal band.
The islands of Calleja are located within the olfactory tubercle in most species; however, in primates these islands are located within the nucleus accumbens, since the olfactory tubercle is absent or extremely rudimentary in the brains of primates
A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen. (caudoputamen in rodent) and continuous with these structures. There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum. Its principle neuron is the medium spiny neuron. Together with the neostriatum (caudate nucleus and putamen), the nucleus accumbens forms the striatum.
a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia[GO][GO:0021768].
The ventral striatopallidal complex in birds corresponds closely to its counterpart in mammals, with a nucleus accumbes present in the rostral telenceaphalon. Note that in birds, a region previously called the nucleus accumbens is now recognized as the lateral part of the bed nucleus of stria terminalis.[ISBN10:0471888893]
Region in the ventral telencephalon, prominent in rodents, but present in all mammals, consisting of a laminated cortical part and the cap/hilus region. It is traditionally viewed as part of the olfactory cortex but recognized by some as having a striatal character. According to many authors, the structure of the OT transitions from cortical like to striatal like along the lateral medial axis. (Maryann Martone)
The olfactory tubercle is a structure involved in Olfaction. It is present in humans, but much smaller than it is in some other animals. It is a frequent subject of research.
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium.
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]
Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer.
The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542].
BTO says dentate gyrus = fascia dentata + hilus. Note that GO classifies dentate gyrus development under hippocampus development
A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces.
TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere
A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO]
Fringe of the tela choroidea of the brain ventricles[MP]
White matter regional part of brain which is flanked by nuclear masses, consisting of both afferent and efferent fibers projecting between the cerebral cortex and the brainstem and spinal cord. It consists of three distinct parts: an anterior limb, posterior limb, and genu. (Adapted from MSH by Maryann Martone).
White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone).
In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells.
The most anterior region the brain including both the telencephalon and diencephalon.
Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]
The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]
In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]
Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.
Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000].
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]
The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]
relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]
From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]
In mammals the cortex covers almost the whole of the cerebral hemispheres.
In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles.
In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum.
In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb.
The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure.
dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight.
Organ component of neuraxis that has as its parts the epithalamus, thalamus, hypothalamus, subthalamus[FMA]. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis).
The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]
Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965].
The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87).
One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG]
Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO]
(...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG]
A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia].
A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO]
Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]
For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG]
Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346.
Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO]
The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG]
Anterior part of the diencephalon that lies between the dorsal thalamus, hypothalamus, and tegmentum of the mesencephalon, including subthalamic nucleus, zona incerta, the fields of Forel, and the nucleus of ansa lenticularis[GO, modified].
Some sources treat the subthalamus as distinct from the thalamus, separated by the zona limitans intrathalamica. In MA, the ventral thalamus is part of the thalamus. Butler Hodos who identify a dorsal to ventral sequence consisting of epithalamus, dorsal thalamus, ventral thalamus and hypothalamus. We solve this by considering dorsal and ventral thalamus distinct, and the label thalamus as being ambiguous w.r.t thalamus proper (dorsal thalamus) or wider thalamus (dorsal plus ventral)
the epithelial lining of the trachea which contains numerous ciliated cells
An epithelium that is part of a small intestine [Automatically generated definition].
Intestinal epithelium which lines the lumen of the mid intestine.[TAO]
The thalamic reticular nucleus is part of the ventral thalamus that forms a capsule around the thalamus laterally. It is separated from the thalamus by the external medullary lamina. Reticular cells are GABAergic, and have discoid dendritic arbors in the plane of the nucleus. Thalamic Reticular Nucleus is variously abbreviated TRN, RTN, NRT, and RT. [WP,unvetted].
only MA considers this part of a subthalamus; MA also considers a subthalamus part of a thalamus
A segment of the epithalamus that has as its parts the lateral and medial habenular nuclei and the habenular commissure.
The habenula relays impulses from limbic areas of the telencephalon to an unpaired midbrain nucleus, the interpeduncular nucleus.[TAO]
A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399).
A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO]
Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO]
relationship loss: part_of pineal complex (TAO:0001359)[TAO]
The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG]
lobulated in humans, homogeneous in mouse. Calcifies with age in humans.
The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO].
Lens shaped nucleus lying in the subthalamu[NIFSTD:nlx_anat_1010002]s
The zona incerta is a horizontally elongated region of gray matter cells in the subthalamus below the thalamus. Its connections project extensively over the brain from the cerebral cortex down into the spinal cord. Its function is unknown though several have been proposed related to 'limbic–motor integration' such as controlling visceral activity and pain; gating sensory input and synchronizing cortical and subcortical brain rhythms. Its dysfunction may play a role in central pain syndrome. It is also been identified as a promising deep brain stimulation therapy target for treating Parkinsons Disease. Its existence was first described by Auguste Forel in 1877 as a 'region of which nothing certain can be said'. A hundred and thirty years later in 2007, Nadia Urbain and Martin Deschênes of Université Laval noted that the 'zona incerta is among the least studied regions of the brain; its name does not even appear in the index of many textbooks. ' [WP,unvetted].
Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF].
relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'
The habenular commissure, is a brain commissure (a band of nerve fibers) situated in front of the pineal gland that connects the habenular nucleus on one side of the diencephalon with that on the other side. The habernular commissure is part of the trigonum habenulæ (a small depressed triangular area situated in front of the superior colliculus and on the lateral aspect of the posterior part of the tænia thalami). The trigonum habenulæ also contains groups of nerve cells termed the ganglion habenulæ. Fibers enter the trigonum habenulæ from the stalk of the pineal gland, and the habenular commissure. Most of the trigonum habenulæ's fibers are, however, directed downward and form a bundle, the fasciculus retroflexus of Meynert, which passes medial to the red nucleus, and, after decussating with the corresponding fasciculus of the opposite side, ends in the interpeduncular ganglion. Nerve cell fibers enter the trigonum habenulæ from the stalk of the pineal body, and the habernular commissure. [WP,unvetted].
The Medial forebrain bundle (MFB), is a complex bundle of axons coming from the basal olfactory regions, the periamygdaloid region, and the septal nuclei, and passing to the lateral hypothalamus, with some carrying on into the tegmentum. It contains both ascending and descending fibers. It also represents a part of the mesolimbic pathway, carrying information between the ventral tegmentum and the nucleus accumbens. It is commonly accepted that the MFB is a part of the reward system, involved in the integration of reward and pleasure. Electrical stimulation of the medial forebrain bundle is believed to cause sensations of pleasure. This hypothesis is based upon intracranial self-stimulation (ICSS) studies. Animals will work for MFB ICSS, and humans report that MFB ICSS is intensely pleasurable. This is most likely because the medial forebrain bundle carries information from the ventral tegmental area (VTA) to the nucleus accumbens (nAcc or Acb). The nAcc is a recognized reward center, and activation of the pathway from the VTA to the nAcc is believed to be rewarding, which is why it is sometimes referred to as the hedonic highway. [WP,unvetted].
fasciculus longitudinalis telencephali medialis
A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.
Originally this was classified as a female reproductive structure, as it was in the MP in 2011
Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]
The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts
The male Dayak fruit bat has lactating mammary glands
The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.
The BTO class represents the combination of nipple plus lobe
The FMA class represents an individule lobe. The nipple is not a part
The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts
Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA]
TODO - ensure correct terminology for lobes/lobules. In mouse there are no distinct lobes (ISBN10:0123813611), here lobule appears to be synonymous with acinus
Secretion produced by the mammary gland.[FMA]
ncit:Milk refers specifically to cow milk
The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates.
we follow in MA in making this is a sib of mammary gland milk, rather than a subclass.
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of an arteriole [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
An endothelium that is part of a venule [Automatically generated definition].
An endothelium that is part of a vein [Automatically generated definition].
The nucleus paraventricularis anterior thalami and nuclues paraventricularis posterior thalami, two of the nuclei mediani thalami; they are situated on the dorsomedial wall of the thalamus, juxtaposed to the third ventricle.
A small cell group in the interthalamic adhesion of the thalamus that occupy the midline region of the internal medullary lamina, between the left and right paracentral nuclei.
central medial nucleus thalamus (rioch 1928)
one of the intralaminar nuclei of the thalamus, located medial to the central lateral nucleus.
nucleus centralis lateralis superior (kusama)
paracentral nucleus thalamus (gurdjian 1927)
The ventral lateral nucleus (VL) is a nucleus of the thalamus. [WP,unvetted].
the group of neurons that serve as the primary processor of visual information received from the retina via the optic tract and send processed information to the visual cortex of the occipital lobe
BTO has distinct classes for body and nucleus, but other sources treat as identical
Nuclear complex of the thalamus situated on the caudal, subpial aspect of the thalamus (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 622).
medial geniculate complex of dorsal thalamus
Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus[ZFA].
Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus. See Figure 7, Atlas of Early Zebrafish Brain Development.[TAO]
The supraoptic nucleus (SON) is a nucleus of magnocellular neurosecretory cells in the hypothalamus of the mammalian brain. The nucleus is situated at the base of the brain, adjacent to the optic chiasm. [WP,unvetted].
Nucleus in the anterior part of the hypothalamus. (MSH) * one of the magnocellular hypothalamic nuclei, an elongated plate of large, deeply staining cells located close to the third ventricle in the anterior hypothalamic area; major source of oxytocin and to a lesser extent, of antidiuretic hormone, neurohormones, which are carried to the neurohypophysis along the paraventriculohypophysial tract. (CSP)
paraventricular nucleus hypothalamus (Malone)
paraventricular nucleus of the hypothalamus
The lateral preoptic nucleus is lateral to the medial preoptic nucleus. It also mediates non-REM sleep onset.[WP,unvetted].
The arcuate nucleus (or infundibular nucleus) is an aggregation of neurons in the mediobasal hypothalamus, adjacent to the third ventricle and the median eminence. The arcuate nucleus includes several important populations of neurons, including: Neuroendocrine neurons, Centrally-projecting neurons and Others. [WP,unvetted].
the semantics of the BTO class arcuate nucleus are not clear
The Dorsomedial hypothalamic nucleus is a nucleus of the hypothalamus. It is involved in feeding, drinking, and body weight regulation. [WP,unvetted].
dorsomedial nucleus of dorsal hypothalamus
dorsomedial nucleus of intermediate hypothalamus
nucleus dorsomedialis hypothalamicae intermediae
The ventromedial nucleus (sometimes referred to as the ventromedial hypothalamus) is a nucleus of the hypothalamus. [WP,unvetted].
ventromedial nucleus of the hypothalamus
The tuberomammillary nucleus is a subnucleus of the posterior third of the hypothalamus. It consists of, largely, histaminergic and is involved with the control of arousal, sleep and circadian rhythm. Axons of the tuberomammillary nucleus project primarily to the cerebral cortex, thalamus, basal ganglia, basal forebrain, and hypothalamus. The projections to the cerebral cortex directly increase cortical activation and arousal, and projections to acetylcholinergic neurons of the basal forebrain and dorsal pons do so indirectly, by increasing the release of acetylcholine in the cerebral cortex. [WP,unvetted].
nucleus habenularis lateralis epithalami
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
Region between dorsal thalamus and optic tectum[pub]. It receives binocular sensory input from retinal ganglion cells of the eyes, and is the region responsible for maintaining the pupillary light reflex. [WP,unvetted].
A narrow, transversely oriented rostral zone of the mesencephalic tectum, bounded caudally by the superior colliculus, rostrally by the habenular trigone, and laterally by the pulvinar thalami; the pretectal area contains several nuclei that receive fibers from the optic tract; it has bilateral efferent connections with the Edinger-Westphal nucleus of the oculomotor nuclear complex by way of which it mediates the pupillary light refle[MP:0009637]x
part of diencephalon in ZFA - modify to adjacent here, supported by pub. Note there is some inconsistency in resources between the region vs nuclei - sometimes they are treated equivalent, sometimes separate (e.g. MP)
Part of the midbrain tecturm consisting of paired bodies that sit caudal to the thalamus and surround the pineal gland in the mesencephalon of vertebrate brains. It comprises the rostral aspect of the midbrain, posterior to the periaqueductal gray and adjacent superior the inferior colliculus. The inferior and superior colliculi are known collectively as the corpora quadrigemina (Latin, quadruplet bodies). It consists of several identified cellular layers and also comprises the brachium of the superior colliculus and commissure of supeior colliculus from Wikipedia.org and Neuronames (MM).
The brain structure where the two separate inputs from the two eyes are combined into a single, integrated map.[AAO]
The roof of the midbrain, morphologically visible by the end of the segmentation period. Kimmel et al, 1995.[TAO]
strata (grisea et alba) colliculi cranialis
strata (grisea et alba) colliculi superioris
The term SC is used when discussing mammals, and OT for other vertebrates[WP]. The tectum is a layered structure, with a number of layers that vary by species. The superficial layers are sensory-related, and receive input from the eyes as well as other sensory systems.[1] The optic tectum is one of the fundamental components of the vertebrate brain, existing across the full range of species from hagfish to human.[4] (See the brain article for background.) Some aspects of the structure are very consistent, including a structure composed of a number of layers, with a dense input from the optic nerve to the superficial layers and another strong input conveying somatosensory input to deeper layers. Other aspects are highly variable, such as the total number of layers (from 3 in the African lungfish to 15 in the goldfish[5]), and the number of different types of cells (from 2 in the lungfish to 27 in the house sparrow[5]). In hagfish, lamprey, and shark it is a relatively small structure, but in teleost fish it is greatly expanded, in some cases becoming the largest structure in the brain. (See the adjoining drawing of a codfish brain.) In amphibians, reptiles, and especially birds it is also a very significant component, but in mammals it is dwarfed by the massive expansion of the cerebral cortex.
Part of the midbrain tectum, consisting of paired predominantly gray matter elevations on the dorsal aspect of the midbrain, located caudal to the superior colliculus, dorsal to the periaqueductal gray of the cerebral aqueduct and rostral to the cerebellum. According to Neuronames, the inferior colliculus comprises the central, pericentral and external nucleus and two predominantly white matter structures, the brachium of the inferior colliculus and the commissure of the inferior colliculus (MM).
Large round nucleus located in the midbrain tegmentum, consisting of a magnocellular and parvicellular portion in most species studied.
in animals without a significant corticospinal tract, gait is mainly controlled by the red nucleus.
nucleus rotundus subthalamo-peduncularis
A multi-tissue structure that is part of a spinal cord.
A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO].
In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva
The term neocortex refers to those areas of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN)
The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils
An epithelium that is part of a nasopharynx [Automatically generated definition].
epithelial tissue of nasal part of pharynx
An epithelium that is part of a oropharynx [Automatically generated definition].
Composition varies with species and time. This is classified as nonkeratinizing stratified squamous in FMA, unilaminar in EHDAA2; the majority of the pharyngeal epithelium is unilaminar in zebrafish
A modified six-layered cortex between the subiculum and the main part of the parahippocampal gyrus.
A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum.
Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish. The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the 'avian hippocampus'. The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa. One of the consequences of this is that the medial pallium ('hippocampal' zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming 'cognitive maps' of the areas they inhabit.[WP]
An epithelium that is part of a respiratory bronchiole [Automatically generated definition].
bronchiolus respiratorius epithelial tissue
epithelial tissue of bronchiolus respiratorius
epithelial tissue of respiratory bronchiole
respiratory bronchiole epithelial tissue
The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP].
A submucosa that is part of a bronchus [Automatically generated definition].
An epithelium that is part of a terminal bronchiole [Automatically generated definition].
bronchiolus terminalis epithelial tissue
epithelial tissue of bronchiolus terminalis
epithelial tissue of terminal bronchiole
the parenchymatous tissue of the spleen that surrounds splenic blood vessels, consists of compact masses of lymphatic cells and is where foreign material removed from the blood is used to initiate an immune reaction that results in the production of antibodies
The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located. [Wikipedia:White_pulp]
The area of the spleen in which T cells surround the central arteriole
FMA distinguishes periarterial (PALS) from periarteriolar (FMA:62806)
diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO].
todo - add part relationships to specific layers
Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO].
guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002).
A diffuse collection of lymphpoid cells that participate in airway immune responses
Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN10:0123813611] Notes: FMA classifies this as organized, not diffuse
A thoracic nerve that nerve travels into the abdomen, where its fibers synapse in the renal ganglia.
in MA this is part of the kidney but this leads to unsatisfiability
ramus renalis nervus splanchnici minoris
Regional part of substantia nigra consisting of a densely packed region of cells, more or less dorsal to the pars reticulata, but extending into the pars reticulata in some species. The dominant neurotransmitter used by pars compacta neurons is dopamine. Pars compacta neurons are pigmented in many species (MM).
nucleus substantiae nigrae, Pars compacta
Regional part of substantia nigra consisting of loosely packed cells, generally located ventral and lateral to the pars compacta. Many cells in this region use GABA as a neurotransmitter (MM).
the cells of pars reticulata bear a strong structural and functional resemblance to the inner segment of the globus pallidus
A thin extracellular layer that sometimes lies below the basal lamina, is composed chiefly of collagenous fibers, and serves to anchor the basal lamina to underlying connective tissue.
this class represents a continuous sheet of reticular lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'lamina reticularis' represents a portion of substance on the scale of a single cell.
Body substance which consists of spermatozoa and seminal plasma.[FMA]
Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined ain taxonomically generic way (see comments for UBERON:0006530).
Body substance in liquid state contained in the lumen of arterial and venous trees, blood capillary and the cardiac chambers; constitutes the liquid phase of blood.[FMA]
A bodily fluid that is produced by the liver and aids the process of digestion of lipids in the small intestine[WP, modified].
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
A submucosa that is part of a esophagus [Automatically generated definition].
A lamina propria that is part of a esophagus [Automatically generated definition].
A serous membrane that is part of a esophagus [Automatically generated definition].
the epithelial layer that lines the luminal space of the esophagus
TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar
Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]
Body substance derived from plasma by the elimination of fibrinogen.[FMA]
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO]. Subdivision of arterial tree (organ) which is directly continuous with capillary vessel[FMA].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
the tubular intestinal glands found in the mucosal membranes
In histology, an intestinal crypt, also crypt of LieberkC<hn and intestinal gland, is a gland found in the epithelial lining of the small intestine and colon. The crypts secrete various enzymes, including sucrase and maltase, along with endopeptidases and exopeptidases. Also new epithelium is formed here, keeping in mind that the epithelium at this site is frequently worn away by the passing food. Loss of proliferation control in the crypts is thought to lead to colorectal cancer. The basal portion of the Crypt contains multipotent stem cells. At each mitosis one daughter remains a stem cell while the other differentiates and migrates up the side of the crypt and eventually the villus. Goblet cells are among the cells produced in this fashion[Wikipedia:Intestinal_crypt].
Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules
A crypt of lieberkuhn that is part of a large intestine [Automatically generated definition].
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011
Marsupials possess only a rudimentary placenta, with reduced nutrient and oxygen exchanging capabilities.
Portion of semisolid bodily waste discharged through the anus[MW,modified]
Excretion in semisolid state processed by the intestine.[FMA]
Trunk ganglion which is bilaterally paired and located at the anterior end of the sympathetic ganglion chain.
the small ganglion located at the level of the cricoid cartilage of the laryngeal wall
The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things. [WP,unvetted].
Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III.[FMA]
The thicker, deeper layer of the dermis, comprised of criss-crossing collagen fibers that form a strong elastic network and also containing blood and lymph vessels, nerves and nerve endings, and hair follicles
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783].
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]
Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.
A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784].
Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO]
The white fibrocartilages admit of arrangement into four groups—interarticular, connecting, circumferential, and stratiform -- WP. EDITOR NOTE: TODO add mineralized
Cartilage tissue that is flexible and contains abundant elastic fibers.
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785].
Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO]
A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP].
Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO]
relationship loss: part_of principal cavity (AAO:0000992)[AAO]
pseudostratified main olfactory epithelium
Arthrodial joints, with the exception of the first, in which the cartilage is directly united with the sternum, and which is, therefore, a synarthrodial articulation.
FMA has FMA:72323 'Costosternal joint', isa Synchondrosis, no other relationships
Anatomical cluster consisting of the iliacus and the psoas major[WP].
On of the muscles that make up the buttocks: the gluteus maximus muscle, gluteus medius muscle and gluteus minimus muscle.
FMA includes tensor fasciae latae and other buttock muscles. BTO def: Any one of three large skeletal muscles that form the buttock and move the thigh.
Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints.
Interchondral Articulations (articulations of the cartilages of the ribs with each other). The contiguous borders of the sixth, seventh, and eighth, and sometimes those of the ninth and tenth, costal cartilages articulate with each other by small, smooth, oblong facets. Each articulation is enclosed in a thin articular capsule, lined by synovial membrane and strengthened laterally and medially by ligamentous fibers which pass from one cartilage to the other. Sometimes the fifth costal cartilages, more rarely the ninth and tenth, articulate by their lower borders with the adjoining cartilages by small oval facets; more frequently the connection is by a few ligamentous fibers.
Consider creating logical definition after obo2owl cardinality tests
FMA has both synovial and syndesmosis subtypes - consider adding separate class for FMA:7955 Synovial interchondral joint
interchondral joint of 9th and 10th ribs
A cable-like bundle of peripheral axons (the long, slender projections of neurons). A nerve provides a common pathway for the electrochemical nerve impulses that are transmitted along each of the axons. Nerves are found only in the peripheral nervous system. In the central nervous system, the analogous structures are known as tracts[WP].
Neural tree (organ) which is directly continuous with the neuraxis. Examples: phrenic nerve, radial nerve, ilioinguinal nerve, sciatic nerve.
The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO].
most sources classify this as autonomic, but in FMA it is placed directly under nervous system.
Peripheral portion of the lymph node, underneath the capsule[WP].
The mdeullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells.
A plexus of nerves situated at the base of the heart that innervate the heart.
The pulmonary plexus is an autonomic plexus formed from pulmonary branches of vagus nerve and the sympathetic trunk. It supplies the Bronchial tree. [WP,unvetted].
The celiac plexus, also known as the solar plexus, is a complex network of nerves located in the abdomen. The celiac plexus is located near where the celiac trunk, superior mesenteric artery, and renal arteries branch from the abdominal aorta. It is behind the stomach and the omental bursa and in front of the crura of the diaphragm, on the level of the first lumbar vertebra, L1. The plexus is formed (in part) by the greater and lesser splanchnic nerves of both sides, and also parts of the right vagus nerve. The celiac plexus proper consists of the celiac ganglia with a network of interconnecting fibers. The aorticorenal ganglia are often considered to be part of the celiac ganglia, and thus, part of the plexus. [WP,unvetted].
The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted].
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
The superior hypogastric plexus (in older texts, hypogastric plexus or presacral nerve) is a plexus of nerves situated on the vertebral bodies below the bifurcation of the aorta. [WP,unvetted].
check relationship with generic hypogastric nerve/plexus
The inferior hypogastric plexus (pelvic plexus in some texts) is a plexus of nerves that supplies the viscera of the pelvic cavity. The inferior hypogastric plexus is a paired structure, with each situated on the side of the rectum in the male, and at the sides of the rectum and vagina in the female. [WP,unvetted].
the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage
provides some protection from trauma and damage.
The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
the veins that return oxygenated blood from the lungs to the left atrium of the heart
A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO].
Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints).
Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG]
membrana synovialis capsulae articularis
synovial layer of articular capsule of synovial joint
synovial membrane of articular capsule of synovial joint
synovium of articular capsule of synovial joint
A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord.
A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris.
Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO]
In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve
FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2]
Heterogeneous cluster of neural somas in the brain and the spinal cord.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
Posterior part of the cerebral hemisphere (MSH)
Gray matter of the insular region of the neocortex. In gyrencephalic animals, it is part of the insular lobe and lies in the depths of the lateral fissure and covered by portions of the frontal, parietal and temporal lobes. It includes Brodmann areas 13-16.
Consider splitting insular cortex from insular lobe. See https://github.com/obophenotype/uberon/issues/412
two classes in ncit, Central_Lobe is part of temporal lobe
one of the four basal ganglia in each cerebral hemisphere that consists of a thin lamina of gray matter between the lentiform nucleus and the insula[BTO]. The claustrum, which is suspected to be present in all mammals, is a fairly thin (fraction of 1 mm to multiple mms) vertical curved sheet of subcortical gray matter oriented sagittally between the white matter tracts of the external capsule and extreme capsule. The claustrum is lateral to the putamen and medial to the insular cortex and is considered by some sources to be part of the basal ganglia. There are lateral and medial tracts connecting to many cortices and perhaps to the hippocampus, the amygdala, and the caudate nucleus (connections with subcortical centers are a matter of debate)[WP].
The internal carotid plexus (carotid plexus) is situated on the lateral side of the internal carotid artery, and in the plexus there occasionally exists a small gangliform swelling, the carotid ganglion, on the under surface of the artery. Postganglionic sympathetic fibres ascend from the superior cervical ganglion, along the walls of the internal carotid artery, to enter the internal carotid plexus. These fibres then distribute to deep structures, which include the levator palpebrae superioris and pupillary dilator muscles. Some of the fibres from the internal carotid plexus converge to form the deep petrosal nerve. The internal carotid plexus communicates with the semilunar ganglion, the abducent nerve, and the sphenopalatine ganglion; it distributes filaments to the wall of the carotid artery, and also communicates with the tympanic branch of the glossopharyngeal nerve. [WP,unvetted].
the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells
consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells
the layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance
Has cells that produce and secrete bipolar lipids which prevent evaporation, helping to 'water-proof' the skin. Keratinization begins in the stratum spinosum. [Wikipedia:Stratum_spinosum]
the outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells
The keratinized outermost layer of the epidermis, which is periodically shed.[AAO]
this skin layer is composed mainly of dead cells that lack nuclei. As these dead cells slough off on the surface in the thin air-filled stratum disjunctum, they are continuously replaced by new cells from the stratum germinativum (basale). In the human forearm, for example, about 1300 cells/cm2/hr are shed. This outer layer that is sloughed off is also known as the stratum dysjunctum. Cells of the stratum corneum contain keratin, a protein that helps keep the skin hydrated by preventing water evaporation. These cells can also absorb water, further aiding in hydration, and explaining why humans and other animals experience wrinkling of the skin on the fingers and toes ('pruning') when immersed in water for prolonged periods. In addition, this layer is responsible for the 'spring back' or stretchy properties of skin. A weak glutenous protein bond pulls the skin back to its natural shape. The thickness of the stratum corneum varies according to the amount of protection and/or grip required by a region of the body. For example, the hands are typically used to grasp objects, requiring the palms to be covered with a thick stratum corneum. In a similar manner, the sole of the foot is prone to injury, and so it is protected with a thick stratum corneum layer. In general, the stratum corneum contains 15 to 20 layers of dead cells. The stratum corneum has a thickness between 10 and 40 μm. n reptiles, the stratum corneum is permanent, and is replaced only during times of rapid growth, in a process called ecdysis or moulting. The stratum corneum in reptiles contains beta-keratin, which provides a much more rigid skin layer.
some oral epitehlium also has cornified layer / stratum corneum
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
The simple columnar epithelial lining of the gall bladder.
Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip.
a male mouse has no nipples - mammary tissue regresses during embryonic development
FMA makes this part of the breast, whereas in MA it is part of the mammary gland -
An epithelium that is part of a bronchus [Automatically generated definition].
Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple.[FMA]
tiny muscle fiber attached to each hair follicle, which contract to make the hairs stand on end, causing goose bumps. They exist in most mammals including humans.
* An ovoid densely packed collection of small cells of the anterior hypothalamus lying close to the midline in a shallow impression of the optic chiasm. (MSH) * small group of nerve cell bodies in the supraoptic region of the hypothalamus, just above the optic chiasm; influences rhythmic aspects of hypothalamic functions in many vertebrate species. (CSP)
The medial preoptic nucleus is bounded laterally by the lateral preoptic nucleus, and medially by the preoptic periventricular nucleus. It releases gonadotropin-releasing hormone, controls copulation in males, and is larger in males than in females.[WP,unvetted].
Tissue which consists of striated muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue, Cardiac muscle tissue[FMA].
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]
Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]
However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]
almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem
Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM).
TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA
Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947].
(...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG]
nucleus pigmentosus subthalamo-peduncularis
The Inferior Phrenic Veins drain the diaphragm and follow the course of the inferior phrenic arteries; the right ends in the inferior vena cava; the left is often represented by two branches, one of which ends in the left renal or suprarenal vein, while the other passes in front of the esophageal hiatus in the diaphragm and opens into the inferior vena cava. [WP,unvetted].
In human anatomy, the bronchial arteries help supply the lungs with oxygenated blood. Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. [WP,unvetted].
rami bronchiales partis thoracicae aortae
An endothelium that is part of a lymphatic vessel [Automatically generated definition].
The vascular endothelium that lines the lymph vessels.[TAO]
A large raphe nucleus extending from the anterior part of the pons through the mesencephalon; its neurons are serotoninergic[NIF]. The dorsal raphe nucleus is a part of the raphe nucleus and consists of rostral and caudal subdivisions. The rostral aspect of the dorsal raphe is further divided into interfascicular, ventral, ventrolateral and dorsal subnuclei. The projections of the dorsal raphe have been found to vary topographically, and thus the subnuclei differ in their projections. An increased number of cells in the lateral aspects of the dorsal raphe is characteristic of humans and other primates. [WP,unvetted].
TODO check dorsal vs inferior. ZF has no pons.
nucleus fasciculi longitudinalis medialis
nucleus of the posterior commissure (Darkschewitsch)
One of the dorsal column nuclei, the cuneate nucleus is a wedge-shaped nucleus in the closed part of the medulla oblongata. It contains cells that give rise to the cuneate tubercle, visible on the posterior aspect of the medulla. It lies laterally to the gracile nucleus and medial to the spinal trigeminal nucleus in the medulla. [WP,unvetted].
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
The Pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
Respiration organ that develops as an oupocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
An epithelium that is part of a bronchiole [Automatically generated definition].
in FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however there are two distinct terms for the corresponding epithelium.
A capsule that surrounds a adrenal gland.
the narrow subcapsular outer zone of the adrenal cortex where aldosterone is produced
the wide middle zone of the adrenal cortex that produces cortisol (hydrocortisone)
the inner zone of the adrenal cortex that produces the enzymes that convert pregnenolone, a 21-carbon steroid, to 19-carbon steroids
Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted].
In humans this includes the superior and inferior phrenic arteries
The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1P2 millimeters in diameter and contains approximately 2,500 neurons (adapted from Wikipedia)
The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1–2 millimeters in diameter and contains approximately 2,500 neurons. Preganglionic axons from the Edinger-Westphal nucleus form synapses with these cells. The postganglionic axons run in the short ciliary nerves and innervate two eye muscles: the sphincter pupillae constricts the pupil, known as Miosis. The opposite, Mydriasis, is the dilation of the pupil. the ciliaris muscle contracts, releasing tension on the Zonular Fibers, making the lens more convex, also known as accommodation. Both of these muscles are involuntary – they are controlled by the autonomic nervous system. It is one of four parasympathetic ganglia of the head and neck.. [WP,unvetted][Wikipedia:Ciliary_ganglion].
Little is known about the development of parasympathetic neurons apart from the ciliary ganglion in chicks. Although there are considerable gaps in our knowledge, some of the mechanisms controlling sympathetic and enteric neuron development appear to be conserved between mammals, avians and zebrafish.[uncertain][VHOG]
the ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands
The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted].
Artery which supplies blood via branches to the hindlimbs.[AAO]
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].
Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]
relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]
(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]
GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form
The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart.
Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]
Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]
In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu
In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract
Either of a pair of large transverse venous sinuses that conduct blood from the cardinal veins to the sinus venosus of the vertebrate embryo[BTO].
Bilaterally paired longitudinal vein; the anterior cardinal returns blood from the head, and the posterior cardinal returns it from the trunk; these two vessels join together on each side as the common cardinal vein (duct of Cuvier; misnamed the vitelline vein) that leads across the yolk cell to the heart's sinus venosus. Kimmel et al, 1995.[TAO]
Bilaterally paired longitudinal vein; the anterior cardinal returns blood from the head, and the posterior cardinal returns it from the trunk; these two vessels join together on each side as the common cardinal vein, also known as the duct of Cuvier that leads to the heart's sinus venosus.[AAO]
relationship loss: part_of cardinal system (TAO:0000096)[TAO]
In primitive vertebrates, the basic early embryonic pattern is retained, and blood from anterior and posterior systemic tissues is returned in anterior and posterior cardinal veins, both pairs of veins uniting in common cardinal veins near the heart. In derived vertebrates, the cardinals appear but usually persist only in the embryo, being functionally replaced by alternative adult vessels, the precava and postcava (anterior and posterior venae cavae).[well established][VHOG]
Paired in gnathostomes; with only a vestige of the right duct in the adult hagfish (21) and the left duct atrophying at metamorphosis in the lamprey (22)[PMID:20959416, S1]
One of two paired cardinal veins that return blood from the body of the embryo[Kardong]
Continuation of the caudal vein cranial to the anal pore. The cardinal vein splits into a pair of vessels in the cranial trunk, just caudal to the radix of the aorta. The posterior cardinals each empty into the common cardinal vein. [TAO]
Either of two veins which receive blood as an alternate route from the kidneys.[AAO]
relationship loss: part_of axial vasculature (TAO:0001073)[TAO]
join with the corresponding right and left cardinal veins to form the left common cardinal veins, which empty in the sinus venosus. Most of the posterior cardinal veins regress, what remains of them forms the renal segment of the inferior vena cava and the common iliac veins. Later in the development stages, the posterior cardinal veins are replaced by the subcardinal and supracardinal veins. The subcardinal veins form part of the inferior vena cava, renal veins and gonadal veins. The supracardinal veins form part of the inferior vena cava, the intercostal veins, hemiazygos vein and azygos vein
The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted].
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
A fibrous remnant of the allantoic stalk, a narrow fetal canal connecting the apex of the urinary bladder with the umbilicus located in the space of Retzius, between the transversalis fascia anteriorly and the peritoneum posteriorly. its lumen is normally obliterated during development, transforming the urachus into a solid cord, a functionless remnant that persists throughout life as the median umbilical ligament; failure of complete lumen obliteration may result in distinct congenital urachal remnant anomalies[MP].
A fetal canal connecting the bladder with the allantois, persisting throughout life as a cord (median umbilical ligament). [TFD][VHOG]
the layer of flattened cells containing basophilic granules of keratohyalin and lying just above the stratum spinosum (spiny layer) of the epidermis
The superior pancreaticoduodenal artery is an artery that supplies blood to the duodenum and pancreas. It is a branch of the gastroduodenal artery, which comes from the common hepatic artery of the celiac trunk. The common hepatic itself becomes the proper hepatic after giving off the gastroduodenal artery and goes on to supply the right and left lobes of the liver. The term superior distinguishes the superior pancreaticoduodenal artery from the inferior pancreaticoduodenal artery, which a branch of the superior mesenteric artery. These arteries, together with the pancreatic branches of the splenic artery, form connections or anastomoses with one another, allowing blood to perfuse the pancreas and duodenum through multiple channels. The artery splits into two branches: the anterior superior pancreaticoduodenal artery supplies the anterior margins of the duodenum and pancreas the posterior superior pancreaticoduodenal artery supplies the posterior margins of these organs [WP,unvetted].
The layer of lightly staining corneocytes found between the stratum granulosum and stratum corneum layers; found primarily in the thick epidermis of the palmar and plantar skin and is composed of three to five layers of dead, flattened keratinocytes.
Located between the stratum granulosum and stratum corneum layers, it is composed of three to five layers of dead, flattened keratinocytes. The keratinocytes of the stratum lucidum do not feature distinct boundaries and are filled with eleidin, an intermediate form of keratin.
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO].
The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG]
The non-growing portion of a hair which protrudes from the skin, i.e., from the follicle[BTO]. the cuticle, and/or cortex and/or medulla of a hair[MP].
TODO - add distinct subclasses for coat hair vs vibrissa hair
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs
A cortex that is part of a hair [Automatically generated definition].
A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]
The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]
A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve.
Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]
The chamber of the heart that receives blood from the lungs[XAO:EJS].
Right cardiac chamber which is continuous with the pulmonary arterial trunk.[FMA]
The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]
Cardiac chamber which consists of a wall that surrounds the cavity of an atrium.[FMA]
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
Cardiac chamber which consists of a wall that surrounds the cavity of a ventricle.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
The vascular channel in the fetus passing through the liver and joining the umbilical vein with the inferior vena cava.
The vascular channel in the fetus passing through the liver and joining the umbilical vein with the inferior vena cava. [TFD][VHOG]
Ductus venosus naturally closes during the first week of life in most full-term neonates; however, it may take much longer to close in pre-term neonates. Functional closure occurs within minutes of birth. Structural closure in term babies occurs within 3 to 7 days. After it closes, the remnant is known as ligamentum venosum
Left cardiac chamber which is continuous with the aorta.[FMA]
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]
Cardiac septum which separates the right atrium from the left atrium.[FMA]
The partition separating the right and left atria of the heart. [TFD][VHOG]
A valve at the opening of the sinus venosus into the primordial atrium[TFD,modified]
in humans and mouse this is the opening from SV into right atrium. This class represents the valve connecting the SV to any atrium and is applicable to animals with a single atrium
The part of the heart connecting the atrium to the cardiac ventricle[ZFA]. In the developing heart, the constriction between the atrium and ventricle constitutes the atrial canal, and indicates the site of the future atrioventricular valves[WP].
The canal connecting the primitive atrium and ventricle in fishes and amniotes embryo. [TFD][VHOG]
The heart is the first organ to form and function in a vertebrate. (...) Septation of the AV canal is initiated with the formation of inferior and superior endocardial cushions in response to signaling from the overlying myocardium. (...) Analysis of zebrafish mutants with cardiovascular defects uncovered a previously unexpected level of conservation between zebrafish and human cardiovascular physiology.[uncertain][VHOG]
The right side of the AVC becomes the tricuspid valve whereas the left side of the AVC will become the bicuspid valve
The lateral thoracic vein is a tributary of the axillary vein. It runs with the lateral thoracic artery and drains the serratus ventralis muscle and the Pectoralis major muscle. Normally, the thoracoepigastric vein exists between this vein and superficial epigastric vein (a tributary of femoral vein), to act as a shunt for blood if the portal system (through the liver) develops hypertension or a blockage. [WP,unvetted].
The post-cranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer.
The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]
A dura mater that is part of a spinal cord [Automatically generated definition].
Cardiac septum which separates the right ventricle from the left ventricle.[FMA]
The partition separating the right and left ventricles of the heart. [TFD][VHOG]
The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]
involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)
Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon.
in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery.
Nonparenchymatous organ that consists of the dermis and epidermis. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body.[FMA].
consider 'integumentary system' for invertebrates
Note that FMA uses 'skin' for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin
The apex of the heart is the lowest superficial part of the heart. It is directed downward, forward, and to the left, and is overlapped by the left lung and pleura. [WP,unvetted].
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]
A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts.
Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm
Upper limb, which connects the manus with the pectoral girdle.[AAO]
note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb
A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts.
Lower limb, which connects the pes with the pelvic girdle.[AAO]
note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton
The sensory system subserving the sense of vision.
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
the organ that functions to filter blood and to store red corpuscles and platelets
An organ involved in red blood cell filtration and immune response.[AAO]
With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)
It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
this is a 'set of anatomical planes' in FMA
An organ that aids digestion and stores bile produced by the liver[WP].
Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]
The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]
Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition].
A paired organ of the urinary tract which has the production of urine as its primary function.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
In humans, the duodenum is a hollow jointed tube about 10–15 inches (25–38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
the portion of the small intestine that extends from the duodenum to the ileum
TODO consider ZFA:0001323 mid intestine, see also small intestine
The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum]
the portion of the small intestine that extends from the jejunum to the colon
TODO consider ZFA:0000706 posterior intestine, see also colon
The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum]
An ovary that is part of a right side of organism [Automatically generated definition].
An ovary that is part of a left side of organism [Automatically generated definition].
In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].
A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]
Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]
The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]
In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
The fibrous connective tissue surrounding the thymus.
the outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes
Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP]
Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size.
The basic structural unit of the thymus.
The solitary tract and nucleus are structures in the brainstem that carry and receive visceral sensation and taste from the facial (VII), glossopharyngeal (IX) and vagus (X) cranial nerves. [WP,unvetted].
largest nucleus situated in the olivary body, part of the medulla oblongata. It is closely associated with the cerebellum, but its specific function is voluntary body movements.
The inferior olive appears to be present in all vertebrate classes and is particularly well developed in species with a well-developed cerebellum.[well established][VHOG]
complexus olivaris inferior; nuclei olivares inferiores
A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system.
In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]
The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.
superior olivary nucleus (Barr & Kiernan)
The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer.
The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695].
The circuits in the cerebellar cortex look similar across all classes of vertebrates, including fish, reptiles, birds, and mammals (e.g., Fig. 2). This has been taken as evidence that the cerebellum performs functions important to all vertebrate species. (Wikipedia)
The gray matter nuclei located in the center of the cerebellum, embedded in the white matter, which receive inhibitory (GABAergic) inputs from Purkinje cells in the cerebellar cortex and excitatory (glutamatergic) inputs from mossy fiber pathways; all output fibers of the cerebellum originate from the these nuclei[MP]
the region of the cerebellum that is anterior to the primary fissure
responsible for mediating unconscious proprioception.[Wikipedia:Anterior_lobe_of_cerebellum]
the largest and most lateral of the deep cerebellum nuclei; it receives axons of Purkinje cells in the lateral cerebellar hemisphere (neocerebellum) and receives its afferents from the premotor cortex and the supplementary motor cortex through the pontocerebellar system, and its efferents project through the superior cerebellar peduncle and is a major source of its fibers
One or more deep cerebellar nuclei appear in agnathans, sharks, ropefishes, lungfishes, Latimeria, and amphibians. Reptiles have two nuclei (a medial and a lateral), and birds and mammals have three nuclei (a medial, a lateral, and an interposed nucleus). The medial nucleus of mammals is known as the fastigial nucleus, and the lateral nucleus is known as the dentate nucleus.[well established][VHOG]
Cardiac valve which has as its parts the leaf of cardiac valve that separates the atrium from the ventricle.
The atrioventricular valve has four distinct leaflets oriented anterior, posterior, left, and right of the atrioventricular orifice. Hu et al. 2001.[TAO]
Valve in the heart through which blood flows from the atria to the ventricles. [TFD][VHOG]
The conus arteriosus is the most distal part of the primitive fish heart and forms the connection between the ventricle and the ventral aorta. At the sinoatrial, the atrioventricular, and the ventriculoconal junctions, valves developed to prevent backflow of blood during relaxation of the preceding compartment.[uncertain][VHOG]
in ZFA this is part of both atrium and ventricle, but we use a connecting relationship here; see also notes for left and right.
Atrioventricular valve which has as its parts the anterior, posterior and septal leaflets, attached to the fibrous ring of tricuspid valve.[FMA]
The three-segmented valve of the heart that keeps blood in the right ventricle from flowing back into the right atrium. [TFD][VHOG]
The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG]
Atrioventricular valve which has as its parts the anterior and posterior leaflets, attached to the fibrous ring of mitral valve.[FMA]
A valve of the heart, composed of two triangular flaps, that is located between the left atrium and left ventricle and regulates blood flow between these chambers. [TFD][VHOG]
Layer of the dentate gyrus lying deep to the granule cell layer, within the opening of the C or V formed by the granule cell layer characterized by loosely packed polymorphic cells
Cardiac valve which has as its parts the anterior, right posterior and left posterior cusps, attached to the fibrous ring of aortic valve.[FMA]
The valve between the left ventricle of the heart and the ascending aorta, consisting of three semilunar cusps. [TFD][VHOG]
Human variation: It is normally tricuspid (with three leaflets), although in 1% of the population it is found to be congenitally bicuspid (two leaflets)
White matter tract containing fibers projecting from the habenular nuclei to the interpeduncular nucleus (Maryann Martone)
The subcommissural organ is a circumventricular organ consisting of ependymal cells which secrete SCO-spondin[WP,partially vetted].
Occurs throughout the vertebartes [PMID:9579598, http://dx.doi.org/10.1002/ar.1091260210]. First appears in hagfish(Olsson). In many species, including the human, it reaches its full development during embryonic life[PMID:9579598]. During the course of phyletic evolution, one notes various changes. Indeed, in lower vertebrates, the SCO presents a greater degree of enzyme activity than the ependyma while in birds the ependyma demonstrates a more intense activity than the SCO[PMID:479574] Sometimes preceded by flexural organ[doi:10.1007/BF00303086]
Cholinergic cell group that is located ventral to the brachium of the inferior colliculus (in rat) and has reciprocal connectivity with the superior colliculus (Adapted from Paxinos, The rat central nervous system, 2nd ed, 1995, pg 865
Nucleus isthmi is present in the isthmus in most vertebrates. It is called the parabigeminal nucleus in mammals (reference 1); In sum, our results show that the origin of neurons of some tegmental hindbrain nuclei, namely, nucleus isthmi/superior reticular nucleus and secondary gustatory/viscerosensory nucleus is in the URL (upper rhombic lip), and that the temporal order of cell types produced by the URL and their developmental program are conserved among vertebrate species (reference 2).[well established][VHOG]
in MA this is part of the tegmentum/brainstem
Nucleus that is part of the oculomotor nerve complex consisting of preganglionic parasympathetic neurons situated close to the midline at the level of the superior colliculus (Heimer, the Human Brain and Spinal Cord, 1994, pg 244)
edinger-Westphal nucleus of oculomotor nerve
nuclei accessorii nervi oculomtorii (Edinger-Westphal)
nucleus nervi oculomotorii Edinger-Westphal
nucleus nervi oculomotorii parvocellularis
The pedunculopontine nucleus (PPN) (or pedunculopontine tegmental nucleus, PPTN) is located in the brainstem, caudal to the substantia nigra and adjacent to the superior cerebellar peduncle. It is composed by a wide variety of neurochemical cell types, including cholinergic, glutamatergic and GABAergic cells. In the classical sense, the PPN is considered to be one of the main components of the reticular activating system. [WP,unvetted].
A group of neuron cell bodies that form a thin, caplike configuration over the dorsolateral aspect of the crus cerebri; many of its cells are acetylcholinesterase positive.
FMA and NIF support this being part of midbrain tegmentum; MA places this in the thalamus and ABA supports thalamus. todo - check. for now we take a conservative position and assert overlaps for both rather than part of
Cardiac valve which has as its parts the right anterior, left anterior and posterior cusps, attached to the fibrous ring of pulmonary valve.[FMA]
The valve with semilunar cusps at the entrance to the pulmonary trunk from the right ventricle of the heart. [TFD][VHOG]
tegmental reticular nucleus, pontine gray
The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
TODO - check ZFA/pons. also GO says part of dorsorostral pons
Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).
A composite structure of the brain stem, which in NeuroNames is subdivided into the superior cerebellar peduncle of pons, the decussation of superior cerebellar peduncle and the superior cerebellar peduncle of midbrain (MM).
we follow NIF in dividing this into 3 parts. This allows for consistency with ABA
we make the TAO class disjoint for now as it's not clear if this is the analagous structure
superior cerebellar peduncle (Galen, Stilling)
superior cerebellar peduncle (brachium conjuctivum)
superior cerebellar peduncle (brachium conjunctivum)
tractus cerebello-tegmentalis mesencephali
Nuclei in the basal pons, intermingled among the descending axons from the cortex, that receive neocrotcial input and give rise to many axons that cross the midline to enter the contralateral cerebellum (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 135)
Regional part of medullary white matter (according to Neuronames) primarily found at the level of the pons, consisting of a very large bundle of fibers originating in the pontine nuclei projecting to the cerebellum (MM).
brachium pontis (stem of middle cerebellar peduncle)
the most medial of the cerebellar nuclei; it receives its afferent input from Purkinje cells of the flocculonodular lobe and the vermis, and most of its efferent connections travel via the inferior cerebellar peduncle to the vestibular nuclei and to the medullary reticular formation
A nucleus of the lateral medullary nuclear complex.
in ABA this is disjoint from MDR, but we relax this here to accomodate FMA
nucleus reticularis lateralis medullae oblongatae
Nucleus located in the rostral ventrolateral medulla. The PGL was originally identified by cytoarchitectural criteria in the human medulla (Olszewski and Baxter, 1954). In humans, the PGL is located in the ventrolateral quadrant of the rostral medullary tegmentum between the nucleus subtrigeminalis caudally, trapezoid body and the superior olive rostrally, nucleus gigantocellularis medially, spinothalamic tract fibers laterally, inferior olive ventrally, and the nucleus ambiguous dorsally (Olszewski and Baxter, 1954). In the rat, the PGL has been further subdivided into retrofacial PGL (caudal to the facial nucleus), and more rostrally located juxtafacial PGL (medial to the facial nucleus), based upon different connectivity.
The nucleus raphe magnus, located directly rostral to the raphe obscurus, is afferently stimulated from axons in the spinal cord and cerebellum. This makes the magnus a likely candidate for part of the motor system; however, it seems to participate in the endogenous analgesia system. The magnus receives descending afferents from the periaqueductal gray, the paraventricular hypothalamic nucleus, central nucleus of the amygdala, lateral hypothalamic area, parvocellular reticular nucleus and the prelimbic, infralimbic, medial and lateral precentral cortices . All of these brain areas influence the main function of the raphe magnus. The main function of the magnus is mostly pain mediation; in fact it sends projections to the dorsal horn of the spinal cord to directly inhibit pain. The periaquiductal gray, the epicenter of analgesia, sends efferent connections to the nucleus raphe magnus in when it is stimulated by opiates (endogenous or otherwise). Electrical stimulation of the PAG produces analgesia, as well as administration of morphine to the PAG or n.r. magnus. The antinociceptic effects of electrical stimulation of the PAG can be blocked by administering naloxone, an opiate antagonist, to the n.r. magnus. All of this seems to indicate that the magnus is part of the endogenous opiate system, and acts to inhibit pain in the spinal cord. [WP,unvetted].
The nucleus raphe pallidus receives afferent connections from the periaqueductal gray, the paraventricular hypothalamic nucleus, central nucleus of the amygdala, lateral hypothalamic area, and parvocellular reticular nucleus. Also, the pallidus receives afferents from the medial preoptic area, median preoptic nucleus and lateral paragigantocellular reticular nuclei . The pallidus has recently been shown to be involved in the activation of a fever as an immunoreaction. It has been implied that the preoptic area is constantly inhibiting the raphe pallidus, especially the rostral portion, with GABA. When the preoptic area receives immune signals from the body, the inhibition stops and the rostral portion of the raphe pallidus excites the intermediolateral cell column, which induces a fever . The raphe pallidus has also been known to mediate the tachycardia response, an extremely high heart rate known to be incited by emotional or psychological stress. Microinjections of a GABA-a antagonist into the raphe pallidus, induces an increased heart rate. Conversely, microinjections of muscimol, a GABA-a agonist, inhibit tachycardia in rats under air-stress stimuli. In both of these cases, GABA is mediating two different sympathetic responses, so clearly the nucleus raphe pallidus is a far more a complex nucleus than previously thought. [WP,unvetted].
The inferior olivary nucleus that consists of the major laminar structure.
inferior olivary complex, principal olive
inferior olivary complex principal olive
The inferior olivary nucleus that lies between the primary olivary nucleus and the pyramid, and forms a curved lamina, the concavity of which is directed laterally
inferior olivary complex, medial accessory olive
medial accessory inferior olivary nucleus
Nucleus in the caudal medulla that receive projections primarily from ipsilateral dorsal root ganglion cells via the posterior column of the spinal cord
in species with reduced hindlimbs (e.g. cetaceans) the size of this nucleus is reduced
A small, rounded eminence on each side of the FOURTH VENTRICLE, which receives nerve fibers from the SOLITARY NUCLEUS , SPINAL CORD, and adjacent areas of the MEDULLA. The area postrema lies outside the BLOOD-BRAIN BARRIER and its functions include acting as an emetic chemoreceptor.
An area of medulla oblongata, outside the blood-brain barrier. The apical terminals of the neurons are, in a strategic location either to monitor the chemical constitution of the plasma or to release neurogenic substances into the general circulation. Ma 1997.[TAO]
Regional part of medullary white matter (according to Neuronames) primarily found at the level of the open medulla, consisting of a large bundle of fibers projecting to and projecting from the cerebellum. The icp is continuous with the dorsal spinocerebellar tract and also contains a large number of fibers originating in the inferior olivary complex (MM).
inferior cerebellar peduncle (restiform body)
A long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the optic tectum towards target cells in the premotor reticulospinal system in the hindbrain.
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber[FMA].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
Lung which consists of the left upper lobe and left lower lobe.[FMA]
The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters
The lobe of the right lung that is closest to the head.
The lobe of the right lung that is furtherst from the head.
the respiratory conducting tubes distal to the respiratory bronchiole that lead to the alveolar sacs and the alveoli
In human anatomy, respiratory bronchioles exists proximal to the alveolar ducts. The epithelial lining consists of smooth muscle knobs covered by nonciliated, simple cuboidal cells. The smooth muscle constricts under parasympathetic innervation and relax under sympathetic innervation
In the human, the right lung is divided into three lobes (as opposed to two lobes on the left), superior, middle, and inferior, by two interlobular fissures: [WP,unvetted].
The intermediolateral nucleus is a region of gray matter found in Rexed lamina VII of the spinal column. Rexed Lamina VII contains several well defined nuclei including the nucleus dorsalis, the intermediolateral cell column (lateral gray horn), and the sacral autonomic nucleus. It extends from the first thoracic through the third lumbar segment, and contains the autonomic motor neurons that give rise to the preganglionic fibers of the sympathetic system. [WP,unvetted].
intermediolateral nucleus of spinal cord
nucleus intermediolateralis medullae spinalis
The most lateral of the bundles of the anterior nerve roots is generally taken as a dividing line that separates the antero-lateral region into two parts, viz. , an anterior funiculus, between the anterior median fissure and the most lateral of the anterior nerve roots; and a lateral funiculus, between the exit of these roots and the postero-lateral sulcus. [WP,unvetted].
Gelatinous-appearing material in the dorsal horn of the spinal cord, consisting chiefly of Golgi type II neurons and some larger nerve cells, corresponding to Rexed lamina II.
central gelatinous substance of spinal cord
gelatinous substance of dorsal horn of spinal cord
gelatinous substance of posterior horn of spinal cord
substantia gelatinosa cornu posterioris medullae spinalis
substantia gelatinosa of spinal cord dorsal horn
substantia gelatinosa of spinal cord posterior horn
In humans, histologically identical to trachea.
The lobar bronchus is the major airway within the respiratory tree that starts by division of the principal bronchi on both sides and ends at the point of its own subdivision into tertiary or segmental bronchi[GO].
They have relatively large lumens that are lined by respiratory epithelium. There is a smooth muscle layer below the epithelium arranged as two ribbons of muscle that spiral in opposite directions. This smooth muscle layer contains seromucous glands. Irregularly arranged plates of hyaline cartilage surround the smooth muscle. These plates give structural support to the bronchus and maintain the patency of the lumen.
The tertiary bronchi (also known as the segmental bronchi) arise from the secondary bronchi. The respiratory epithelium lining their lumen is surrounded by a layer of smooth muscle. This layer is composed of two ribbons of smooth muscle that spiral in opposite directions. The smooth muscle layer is surrounded by irregular plates of hyaline cartilage which help maintain the patency of the airway. Each of the tertiary bronchi serves a specific bronchopulmonary segment. There are 10 tertiary bronchi in the right lung, and eight in the left. The tertiary bronchi get smaller and divide into primary bronchioles. [WP,unvetted].
the upper conducting airways of the lung; these airways arise from the terminus of the trachea
Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching
lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer
the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls
A bronchiole that is the first segment of the respiratory zone.
mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468)
The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum]
In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region
in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum
The narrow cleft along the medial wall of the lateral ventricle along the margins of which the choroid plexus is attached; it lies between the upper surface of the thalamus and lateral edge of the fornix in the central part of the ventricle and between the terminal stria and fimbria hippocampi in the inferior horn[ZFA].
not to be confused with optic fissure. the choroidal fissure is a subarachnoid space (via subarachnoid fissure in FMA)
Most ontologies appear to have switched to using less confusing primary terms for optic and choroidal fissues. Still need to check FMA - two possible terms? CARO - is this a groove or a space or a line?
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers.
from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP]
Membranous process coming from capsule of lymph node[WP].
The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA].
Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]
The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO]
It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish
While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke’s pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175].
anterior hypothalamic area posterior part
anterior hypothalamic area, posterior part
Elevation on the ventral surface of the brain located at the zone of attachment between the hypothalamic floor and the hypophysis (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg. 446).
median eminence of posterior lobe of pituitary gland
The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon.
request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'
The infundibular part of the pituitary gland consisting of two regions.[AAO]
todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19)
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Vasculature that is part of a head [Automatically generated definition].
A vasculature that is part of a trunk [Automatically generated definition].
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
The cranial most segment of the sternum. Located ventrally with a quadrangular shape, wider superiorly and narrower inferiorly, it articulates with the clavicles and the first two ribs[MP,WP].
One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455).
A cartilaginous extension to the distal part of the sternum.
this class may represent a mixed bony-cartilage element, or it may be the superclass of either purely cartilage or purely ossified elements
usually ossified in the adult human. By age 15 to 29, the xiphoid usually fuses to the body of the sternum with a fibrous joint. Unlike the synovial articulation of major joints, this is non-movable. Much the way the first seven ribs articulate with the sternum, the cartilage in the celiac plexus joins on the xiphoid process, reinforcing it, and indirectly attaches the costal cartilage to the sternum.
one of the bony segments of the sternum[TFD].
Note that some definitions state that this a segment of the primordial sternum.
Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA]
A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO]
Fibrous joint in which the articulating bones or cartilages of the vertebral column and the limbs as well as articulating ossicles, are connected by skeletal ligaments or membranes. Examples: Intervertebral syndesmosis, inferior tibiofibular joint.[FMA]
A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system.
We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots.
The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS].
FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots
the oval neuroepithelial sensory receptor in the anterior wall of the saccule; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies
macula of sacculus (labyrinthus vestibularis)
sacculus (labyrinthus vestibularis) macula
macula of saccule of membranous labyrinth
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]
the neuroepithelial sensory receptor in the inferolateral wall of the utricle; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies; normally sensitive to linear acceleration in the longitudinal axis of the body and to gravitational influences
macula of utriculus (labyrinthus vestibularis)
utriculus (labyrinthus vestibularis) macula
macula of utricle of membranous labyrinth
Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA]
WP considers epiphyseal plates as subtypes of this
consider adding link to hyaline cartilage
Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
A C-shaped membranous bone that provides physical support to the tympanic membrane. The tympanic ring develops sequentially from an initial primordium in the first branchial arch growing in a circumferential fashion around the first pharyngeal cleft into the second branchial arch (Mallo and Gridley, 1996). In most mammals, the tympanic ring exists only during embryonic life, when it coordinates proper development and positioning of the eardrum (see below), and then becomes integrated into the temporal bone[PMID].
Funnel-like ring structure located lateral to the ventral ramus of the squamosal, beneath the skin; it provides support to the tympanic membrane.[AAO]
relationship loss: part_of plectral apparatus (AAO:0000443)[AAO]
in AAO 'Funnel-like ring structure located lateral to the ventral ramus of the squamosal, beneath the skin; it provides support to the tympanic membrane'.
in FMA, the tympanic ring is an anatomical line. Howevever http://www.ncbi.nlm.nih.gov/pubmed/11237469 states: 'the tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane'.
Gene notes: Gsc and Prx1 are essential for tympanic ring development
Group of neurons situated on the ventral surface of the fornix at the level of the foramen of Monro in the third ventricle (adapted from Wikipedia via NIF).
induces drinking behavior after stimulation with angiotensin II[MESH].
Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP].
Anatomical structure that is a membranous gap between bones of the skull.[TAO]
Fibrous connective tissue that surrounds cartilage.
Portion of connective tissue which surrounds cartilage.[TAO]
perichondral region of cartilage element
From the posterior wall of the saccule a canal, the ductus endolymphaticus, is given off; this duct is joined by the ductus utriculosaccularis, and then passes along the aquaeductus vestibuli and ends in a blind pouch, the endolymphatic sac, on the posterior surface of the petrous portion of the temporal bone, where it is in contact with the dura mater. Studies suggest that the endolymphatic duct and endolymphatic sac perform both absorptive and secretory, as well as phagocytic and immunodefensive,functions . [WP,unvetted].
The blind extremity of the endolymphatic duct. [TFD][VHOG]
Many adult anamniotes have an endolymphatic duct that opens onto the surface of the head. In other vertebrates, it either is lost or forms a small, deeply seated endolymphatic sac.[well established][VHOG]
Body cavity subdivision which is enclosed by the thoracic wall and the diaphragm[FMA].
The costal margin, sometimes referred to as the costal arch, is the medial margin formed by the false ribs, which in humans is from the eighth rib to the tenth rib.
we treat margin and arch in FMA as equivalent here, as a temporary measure. This may be split in future. We follow MA in making this a part of the rib.
A stiff structural element that separates two liquid-filled tubes that run along the coil of the cochlea, the scala media and the scala tympani[WP].
The organ of Corti (or spiral organ) is the organ in the inner ear of mammals that contains auditory sensory cells, or 'hair cells.' [WP,unvetted].
The auditory hair cells in tetrapods are located in the inner ear in a structure known as the basilar papilla. In mammals this structure (along with some related structure) is called the organ of Corti.[well established][VHOG]
An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses. They protect and support internal organs. In most vertebrates, ribs surround the chest. they enable lungs to expand by expanding the chest, they also protect the lungs, heart, and other internal organs of the thorax. In some animals, especially snakes, ribs may provide support and protection for the entire body.
Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO]
Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO]
The bone of the cranium that lies above and anterior to the occipital bone in some mammals.
consider splitting classes for inter-parietal and post-parietal. postparietals paired in reptiles, fused in mammals.
The head of the rib is the end of a rib closest to the vertebral column, with which it articulates with. It is marked by a kidney-shaped articular surface, divided by a horizontal crest into two facets for articulation with the depression formed on the bodies of two adjacent thoracic vertebrae; the upper facet is the smaller; to the crest is attached the interarticular ligament. [WP,unvetted].
Bowman's glands (aka olfactory glands, glands of Bowman) are situated in the olfactory mucosa, beneath the olfactory epithelium, in the lamina propria, a connective tissue also containing fibroblasts, blood vessels, and bundles of fine axons from the olfactory neurons. The structure of the Bowman's glands consists of an acinus in the lamina propria and a secretory duct going out through the olfactory epithelium. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. Bowman's glands might secrete proteins such as Lysozyme, amylase and IgA similarly to serous glands. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP].
Multicellular mucous glands of the olfactory epithelium, present only in adults.[AAO]
The overlaying membrane of the cochlear duct, an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells; sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair cell membrane potential, transducing sound into electrical signals[MP,modified]
The tectorial membrane (TM) is one of two acellular gels in the cochlea of the inner ear, the other being the basilar membrane (BM). The TM is located above the sulcus spiralis internus and the spiral organ of Corti and extends along the longitudinal length of the cochlea parallel to the BM. Radially the TM is divided into three zones, the limbal, middle and marginal zones. Of these the limbal zone is the thinnest (transversally) and overlies the auditory teeth of Huschke with its inside edge attached to the spiral limbus. The marginal zone is the thickest (transversally) and is divided from the middle zone by Hensen's Stripe. It overlies the sensory inner hair cells and electrically-motile outer hair cells of the organ of Corti and during acoustic stimulation stimulates the inner hair cells through fluid coupling, and the outer hair cells via direct connection to their tallest stereocilia[Wikipedia:Tectorial_membrane_%28cochlea%29].
tectorial membrane of spiral organ of cochlea
A proximal phalanx that is part of a finger [Automatically generated definition].
The tubercle of a rib is an eminence on the posterior surface, at the junction of the neck and body of the rib, and nearer the lower than the upper border. It consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrae to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs[WP].
the nonvascular, resilient, flexible hyaline connective tissue that connects the end of a true rib to the sternum or the end of a false rib with the with the lower border of the costal cartilage above it
A rib that is ventrally connected to the sternum.
A rib that is not directly ventrally connected to the sternum.
A rib that is not connected to sternum or sternal cartilage.
We synonymize 'free rib' with 'floating rib' - this case it referes to caudal ribs, but you can have free ribs (i.e. non-attached ventrally) in other places . Should we just synonymize this with 'floating rib'? see Primate Anatomy: An Introduction by Friderun Ankel-Simons pg. 275
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
covers the brain dorsally in chondrichthyans
the jelly-like substance in the middle of the spinal disc which is a remnant of the notochord
The nucleus pulposus consists of chondrocytes, collagen fibrils, and proteoglycan aggrecans that have hyaluronic long chains which attract water. Attached to each hyaluronic chain are side chains of chondroitin sulfate and keratan sulfate[Wikipedia:Nucleus_pulposus]
nucleus pulposus (diskus intervertebralis)
nucleus propulsus of intervertebral disk
Function noyes: It functions to distribute hydraulic pressure in all directions within each disc under compressive loads.
one of a number of veins in the subcutaneous tissue that empty into deep veins
One of the bones of the upper jaw situated between and in front of the maxillae[VHOG].
requires checking embryonic vs adult; isa fetal organ part in FMA; adult bone of upper jaw in AAO and ZFA; split. Note that we have loops if we add develops_from UBERON:0005620 primary palate
Dermal bone that forms the anteriormost element of the upper jaw. It articulates with the maxilla posterodorsally and its antimere medially. The premaxilla is paired.[TAO]
One of the bones of the upper jaw situated between and in front of the maxillae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Paired, intramembranous bones located at the anterior end of the skull; they form the anterior-most segment of the maxillary arch.[AAO]
relationship loss: overlaps inter-premaxillary joint (TAO:0001950)[TAO]
relationship loss: overlaps mesethmoid-premaxillary joint (TAO:0001676)[TAO]
relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO]
(...) in all higher vertebrates a premaxilla is present (...) (reference 1); Although the presence of a tooth-bearing outer buccal arcade (premaxilla, maxilla, dentary) is cited as a common character of Osteichthyes, dipnoans lack all three bones (...) (reference 2).[well established][VHOG]
A paired regions of the cerebellum that lie outside and lateral to the central vermis[MP]. The cerebellum consists of three parts, a median and two lateral, which are continuous with each other, and are substantially the same in structure. The median portion is constricted, and is called the vermis, from its annulated appearance which it owes to the transverse ridges and furrows upon it; the lateral expanded portions are named the hemispheres. The lateral hemisphere is considered the portion of the cerebellum to develop most recently. [WP,unvetted].
Two column-shaped nuclear masses formed by large cells. Clarke's nuclei are located in the regions dorsolateral to the central canal in the thoratic and upper lumbar segments.
Clarke's column (column of Clarke, dorsal nucleus, posterior thoracic nucleus, nucleus dorsalis of Clarke) is a group of interneurons found in the medial part of Lamina VII, also known as the intermediate zone, of the spinal cord. It is mainly located from the T1 to L3-L4 levels and is an important structure for proprioception[Wikipedia:Posterior_thoracic_nucleus].
dorsal nucleus of the spinal cord rostral part
either one of the pair of tubular extensions from the uterine body where the uterus and the uterine tubes meet; uterine horns are anterior Mullerian duct-derived structures
The uterine horns are far more prominent in other animals than they are in humans
The passage between the venous and arterial mesocardia —i.e., between the aorta and pulmonary artery in front and the superior vena cava behind. Also, the sinus that forms in the pericardial cavity where the dorso-mesentary pericardium reside.[WP,unvetted].
In human anatomy, the popliteal artery is defined as the extension of the 'superficial' femoral artery after passing through the adductor canal and adductor hiatus above the knee. The termination of the popliteal artery is its bifurcation into the anterior tibial artery and posterior tibial artery. The popliteal artery, through numerous smaller branches, supplies blood to the knee joint and muscles in the thigh and calf. It is accompanied, along its length, by the popliteal vein. [WP,unvetted].
The iliocostalis is the muscle immediately lateral to the longissimus that is the nearest to the furrow that separates the epaxial muscles from the hypaxial. It lies very deep to the fleshy portion of the serratus ventralis (serratus anterior). [WP,unvetted].
A superficial postvertebral muscle innervated by the posterior ramus of the cervical spinal nerve with origins in the upper thoracic and lower cervical spinous processes whose actions are to extend and ipsilaterally rotate the head and neck. Examples: splenius capitis, splenius cervicis
An embryological anatomical structure that forms an open connection between the initial area of development of the thyroid gland and its final position; it is located exactly midline, between the anterior 2/3rds and posterior 1/3rd of the tongue; this duct normally atrophies and closes off as the foramen cecum before birth
An embryonic duct extending between the thyroid primordium and the posterior tongue. [TFD][VHOG]
A duct, called the thyroglossal duct in mammals, is considered to be characteristic of thyroid development. The thyroglossal duct, degenerating in many species during late development, marks the way the thyroid primordium relocates during embryonic development from the pharynx to its position deep in the cervical mesenchyme. We cannot exclude that the duct of the endostyle and the thyroglossal duct may have evolved independently, but as they both represent a more or less persistent connection of the organ to the pharynx, it is likely that they are homologous structures.[well established][VHOG]
An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base.
An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG]
(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG]
Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)
The pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO].
The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO].
The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord].
The portion of the medulla spinalis which lies between the posterolateral sulcus and the posterior median sulcus is named the posterior funiculus. This area includes the dorsal columns (also called the posterior columns) which contains the fasciculus gracilis and, higher in the body, the fasciculus cuneatus, which are separated by a partition of glial cells. Histologically, these two fasciculi are on other sides of the dorsal intermediate sulcus. [WP,unvetted].
ZFA class is undefined. We currently do not place this as part of the DCML pathway as this would lead to taxon constraint violations.
In the brain, the corpora quadrigemina (Latin for 'quadruplet bodies') are the four colliculi—two inferior, two superior—located on the tectum the dorsal aspect of the midbrain. The corpora quadrigemina are reflex centers involving vision and hearing. [WP,unvetted]. Two pairs of colliculi on the dorsal surface of the midbrain composed of white matter externally and gray matter within, the superior pair containing correlation centers for optic reflexes and the inferior pair containing correlation centers for auditory reflexes[BTO].
this section needs worked on for pan-vertebrate consistency. for now we include a mammal specific definition, even though the child terms are applicable across vertebrates
The ventral roots contain efferent motor axons. Similar to the dorsal roots, the ventral roots continue out from the spinal column, and meet and mix with their corresponding dorsal nerve root at a point after the ganglion.
The efferent motor root of a spinal nerve. At its distal end, the ventral root joins with the dorsal root to form a mixed spinal nerve[Wikipedia:Anterior_root_of_spinal_nerve].
FMA:77516 xref is a 'general anatomical term'. We xref both to ensure equivalence.
The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion).
In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve].
The celiac ganglia are two large irregularly shaped masses of nerve tissue in the upper abdomen. Part of the sympathetic subdivision of the autonomic nervous system (ANS), the two celiac ganglia are the largest ganglia in the ANS, and they innervate most of the digestive tract. They have the appearance of lymph glands and are placed on either side of the midline in front of the crura of the diaphragm, close to the suprarenal glands (also called adrenal glands). The ganglion on the right side is placed behind the inferior vena cava. They are sometimes referred to as the semilunar ganglia or the solar ganglia. [WP,unvetted].
The lentiform nucleus or lenticular nucleus comprises the putamen and the globus pallidus within the basal ganglia. It is a large, cone-shaped mass of gray matter just lateral to the internal capsule. [WP,unvetted].
A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO].
Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts
Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO]
Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624].
The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb
Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos)
the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP).
White matter tract that contains projections from the olfactory bulb to other parts of the brain
A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647].
The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia].
Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA]
in animals with a long snout, the olfactory tract is long, whereas it is short in short-snouted animals such as primates. In some birds the tract per se does not exist as the bulb is connected directly to the cerebral hemisphere.[ISBN10:0471888893]
The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa.
Laminated structure lying caudal to the olfactory bulb
The laterodorsal tegmental nucleus (or lateroposterior tegmental nucleus) is a nucleus situated in the brainstem, spanning the midbrain tegmentum and the pontine tegmentum. [WP,unvetted].
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
The pupillary membrane in mammals exists in the fetus as a source of blood supply for the lens. It normally atrophies from the time of birth to the age of four to eight weeks.
An artery that is part of the optic stalk of the eye and extends from the optic disc through the vitreous humor to the lens.
Artery that is internal to the eye. Isogai et al. 2001.[TAO]
In humans, Usually fully regressed before birth, its purpose is to supply nutrient to the developing lens in the growing fetus. During the tenth week of development the lens grows independent of a blood supply and the hyaloid artery usually regresses. Its proximal portion remains as the central artery of the retina. Regression of the hyaloid artery leaves a clear central zone through the vitreous called the hyaloid canal or Cloquet's canal. Occasionally the artery may not fully regress, resulting in the condition persistent hyaloid artery. More commonly, small remnants of the artery may remain. Free remnants can sometimes be seen as 'floaters'. An anterior remnant of the hyaloid artery can be seen in some people as Mittendorf's dot, a small pinpoint-like scar on the posterior surface of the lens. A posterior remnant may be seen where the artery left the optic disc, and is known as Bergmeister's papilla
Periventricular zone of the hypothalamus
Hypothalamic medial zone behavioral control column
The term reticular formation (classical) denotes a composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ).
this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.
FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure
The osseous spiral lamina consists of two plates of bone, and between these are the canals for the transmission of the filaments of the acoustic nerve. On the upper plate of that part of the lamina which is outside the vestibular membrane, the periosteum is thickened to form the limbus spiralis (or limbus laminæ spiralis), this ends externally in a concavity, the sulcus spiralis internus, which represents, on section, the form of the letter C. [WP,unvetted].
A concavity in the floor of the cochlear duct, formed by either the overhanging vestibular lip (inner spiral sulcus) or the spiral prominence and the spiral organ (outer spiral sulcus).
The fluid-filled space separating the membranous from the osseous labyrinth.
At the hinder part of the medial wall of the vestibule is the orifice of the vestibular aqueduct, which extends to the posterior surface of the petrous portion of the temporal bone. It transmits a small vein, and contains a tubular prolongation of the membranous labyrinth, the ductus endolymphaticus, which ends in a cul-de-sac between the layers of the dura mater within the cranial cavity. [WP,unvetted].
Acellular structure composed of calcium carbonate located in the otolith organ.
Portion of organism substance composed of calcium carbonate located in the otolith organ.[TAO]
relationship loss: develops_from immature otolith (TAO:0000139)[TAO]
Currently represented as part of the otolith membrane, but they may also be considered to be embedded in this membrane
A membrane inside the cochlea of the inner ear. It separates scala media from scala vestibuli. Together with the basilar membrane it creates a compartment in the cochlea filled with endolymph, which is important for the function of the organ of Corti. It primarily functions as a diffusion barrier, allowing nutrients to travel from the perilymph to the endolymph of the membranous labyrinth. Histologically, the membrane is composed of two layers of flattened epithelium, separated by a basal lamina. Its structure suggests that its function is transport of fluid and electrolytes.
The upper portion of the spiral ligament contains numerous capillary loops and small blood vessels, and is termed the stria vascularis. It produces endolymph for the scala media, one of the three fluid-filled compartments of the cochlea. [WP,unvetted].
represented as a wall in FMA. MESH def implies part of spiral ligament but better represented as adjacency / overlaps
Portion of tissue (or germinal matrix) upon which the nail rests, the part of the nail bed that extends beneath the nail root and contains nerves, lymph and blood vessels. The matrix is responsible for the production of the cells that become the nail plate. The width and thickness of the nail plate is determined by the size, length, and thickness of the matrix, while the shape of the fingertip itself determines if the nail plate is flat, arched, or hooked. The matrix will continue to grow as long as it receives nutrition and remains in a healthy condition. As new nail plate cells are incubated, they emerge from the matrix round and white to push older nail plate cells forward; and in this way yet older cells become compressed, flat, and translucent, making the pink colour of the capillaries in the nail bed below visible[WP].
Epithelium located beneath the nail plate at the junction between the free edge and the skin of the fingertip. It forms a seal that protects the nail bed.
A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere
The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP].
The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO].
Part of the ventricular system of the brain, forming a single large cavity in the midline of the diencephalon; it is continuous with the lateral ventricles through the interventricular foramen and the fourth ventricle through the cerebral aqueduct. (Maryann Martone)
consider adding class for secondary vesicle precursor
Fluid-filled brain cavity. Kimmel et al, 1995.[TAO]
relationship loss: develops_from forebrain ventricle (TAO:0001259)[TAO]
Recess in third ventricle lying in front of the optic chiasm at the base of the lamina terminalis
At the junction of the floor and anterior wall of the third ventricle, immediately above the optic chiasma, the ventricle presents a small angular recess or diverticulum, the optic recess (or supraoptic recess). [WP,unvetted][Wikipedia:Optic_recess].
The optic recess of the third ventricle, i.e. the pouch of the ventricle penetrating into the interval between the initial optic tracts. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of choroid plexus contained in the third ventricle
chorioid plexus of cerebral hemisphere of third ventricle
third ventricle chorioid plexus of cerebral hemisphere
Part of ventricular system of brain consisting of a narrow channel in the midbrain connecting the third and fourth ventricles. (Maryann Martone)
Two distinct classes in ncit. We classify this as a brain ventricle even though it is not classifically regarded as one (3rd = diencephalon, 4th = hindbrains)
chorioid plexus of cerebral hemisphere of fourth ventricle
fourth ventricle chorioid plexus of cerebral hemisphere
Spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord.
previously mapped to FMA:75364. Note some ontologies (NIF, SNOMED) subdivide this into lumbar, thoracic, etc. Note we follow FMA in distinguishing between the canal and the lumen
The costovertebral joints are the articulations that connect the heads of the ribs with the bodies of the thoracic vertebrae. Joining of ribs to the vertebrae occurs at two places, the head and the tubercle of the rib. Two convex facets from the head attach to two adjacent vertebrae. This forms a trochoid joint, which is strengthened by the ligament of the head and the intercapital ligament. Articulation of the tubercle is to the transverse process of the adjacent vertebrae. This articulation is reinforced by the dorsal costotransverse ligament. [WP,unvetted].
FMA has both this and joint of head of rib
A bars of hyaline cartilage located between the distal part of a rib and a costal cartilage, connecting the ribs to the sternum .
In humans, Joints between costal cartilages of ribs 6-9 are plane synovial joints. Articulation between costal cartilage of rib 9 and rib 10 is fibrous
Anatomical system that consists of the organs and ducts (bile ducts, gallbladder, and associated structures) that are involved in the production and transportation of bile.
the division of the spiral canal of the cochlea that contains the organ of Corti (the neuroepithelial receptor organ for hearing)
located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Scala media houses the organ of Corti. [Wikipedia:Scala_media]
The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA].
The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO]
The yellow or brown waxy secretions produced by vestigial apocrine sweat glands in the external ear canal[MESH].
Cerumen keeps the eardrum pliable, lubricates and cleans the external auditory canal, waterproofs the canal, kills bacteria, and serves as a barrier to trap foreign particles (dust, fungal spores, etc.) by coating the guard hairs of the ear, making them sticky.
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
Spherical outcropping of the respiratory bronchioles and primary site of gas exchange with the blood. Alveoli are particular to mammalian lungs. Different structures are involved in gas exchange in other vertebrates[WP].
A chamber of an organ with cavitated organ parts. Examples: right ventricle of heart, lateral ventricle of brain.
A organ component layer that is part of a neocortex.
the atrial part of middle layer of the heart, comprised of involuntary muscle
An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP].
A central nervous system gray matter layer that is part of a dentate gyrus of hippocampal formation.
The layers of the laminar structure of the hippocampus.
cytoarchitectural fields of hippocampal formation
mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa.
TODO - split nasal vs respiratory tract?
Part of choroid plexus contained in the lateral ventricle
chorioid plexus of cerebral hemisphere of lateral ventricle
lateral ventricle chorioid plexus of cerebral hemisphere
A neural nucleus that is part of the brain.
The medial longitudinal fasciculus (MLF) is a pair of crossed fiber tracts, one on each side of the brainstem. These bundles of axons are situated near the midline of the brainstem and are composed of both ascending and descending fibers that arise from a number of sources and terminate in different areas. [WP,unvetted].
The medial longitudinal fasciculus (MLF) is a pair of crossed fiber tracts (group of axons), that begin with in the nucleus of the MLF and run ventral to the rhombencephalic ventricle, towards the caudal end of the medulla oblongata. The dorsal portion of the MLF including the Mauthner axon continues into the spinal chord while the ventral portion of the MLF associates with other fiber systems in the funiculus ventralis prior to reaching the spinal chord. Throughout the most of its rhombencephalic extent the MLF is intersected by the ventral rhombencephalic commissure[ZFA].
Regional part of fornix consisting of a prominent white matter structure adjacent to the hippocampus on the ventricular side continuous with the alveus. Near the splenium the fimbria separates from the hippocampus as the crus of the fornix. [adapted from Wikipedia] (MM: 2006-10-26).
A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames).
Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM).
The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates.[well established][VHOG]
In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.
Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929].
Multi-tissue structure comprised largely of myelinated axons.[TAO]
The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]
Regional part of cerebellum consisting of the myelinated axons lying deep to the granule cell layer, excluding the deep cerebellar nuclei and the cerebellar peduncles.
CNS white matter that is part of the cerebellum.[TAO]
in NIF this is a composite structure; in MA and FMA it is explicitly part of cerebellum. This leads to consistency problems with strict parcellation schemes like ABA, see cerebellar peduncles. In NIF this is a composite structure, this is followed partially here in weakening the relationship to overlaps
substantia centralis medullaris cerebelli
The regions of the spinal cord that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.
inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries.
WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here.
A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (MUSCLE, SMOOTH, VASCULAR), PHAGOCYTES and the mesangial EXTRACELLULAR MATRIX.
the tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus
check MA part_ofs - should be spatially disjoint from renal glomerulus?
ventral zone of periventricular hypothalamus
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
A muscle organ that is part of a back [Automatically generated definition].
The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes..
A lamina propria that is part of a urethra [Automatically generated definition].
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior–posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and UBERONREF:0000002. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
The connecting cord from the developing embryo to the placenta.
The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP].
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
the duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue
FMA also has 'main submandibular duct' (FMA:59899)
The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO].
not part of a nephron or distal tubule in MA and FMA
White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres.it is subdivided into a genu, a rostrum, a body, and a splenium. (MM)
The largest commissure of the brain connecting the cerebral hemispheres. [TFD][VHOG]
In addition to the anterior commissure, placental mammals have a phylogenetically new forebrain commissure, the corpus callosum, which primarily interconnects the neocortex of the cerebral hemispheres.[well established][VHOG]
The corpus callosum is found only in placental mammals. other groups do have other brain structures that allow for communication between the two hemispheres, such as the anterior commissure, which serves as the primary mode of interhemispheric communication in marsupials.
The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle.
A lamina propria that is part of a bronchus [Automatically generated definition].
lamina propria mucosa of bronchial trunk
lamina propria mucosae of bronchial trunk
The tissue made up of epithelial cells that lines the inside of the lobar bronchus.
An epithelium that is part of a main bronchus [Automatically generated definition].
epithelial tissue of bronchus principalis
An epithelium that is part of a segmental bronchus [Automatically generated definition].
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
distinction between abdomen muscle and abdomen musculature
The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
A thoracic vertebra endochondral element that is composed primarily of a bone tissue.
Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs
a serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]
The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]
the middle layer of the heart, comprised mainly of striated cardiac muscle fibers
TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The middle layer of the heart, consisting of cardiac muscle.[AAO]
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]
EHDAA2 divides the system from the tissue
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA].
WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node.
Subdivision of conducting system of heart which is located in the muscular part of the interatrial septum that is continuous with the atrioventricular bundle.[FMA]
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]
A part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers[GO]
The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle
Subdivision of abdomen, which is demarcated from the abdomen proper by the plane of the superior pelvic aperture, and from the perineum by the inferior surface of the pelvic diaphragm; together with the abdomen proper, it constitutes the abdomen[FMA].
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
Subdivision of trunk proper, which is demarcated from the pelvis by the inferior surface of the pelvic diaphragm and from the lower limbs by the perineofemoral lines; together with the thorax, abdomen, and pelvis, it constitutes the trunk[FMA].
FMA has class anal part of perineum, which may be the same as what EHDAA2 calls perineum
Serous membrane which is divided into parietal and visceral pericardium.
A serous membrane that lines the peritoneal cavity[VHOG,modified].
An epithelium that lines the peritoneal cavity.[TAO]
Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Fibrous_pericardium]
Membrane organ that surrounds the brain and the spinal cord.
consider separate term for meninges aka collection of meninges. Note in EHDAA2 pia mater etc are part of the meninges. Also consider a new class for primary/primitive meninx.
Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG]
Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).
Not consider part of the CNS/neuraxis in FMA
The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals.
consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system
delicate innermost layer of the meninges—the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater].
A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space.
Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections.
the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater].
capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288
in ncit this is divided into periosteal layer and meningeal layer
A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted].
The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG]
The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum
most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint.
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
Any of the small paired racemose glands below the apex of the prostate in males, located posterolateral to the membranous portion of the urethra at the base of the penis, between the two layers of the fascia of the urogenital diaphragm, in the deep perineal pouch, and enclosed by transverse fibers of the sphincter urethrae membranaceae muscle; homologous to the greater vestibular (Bartholin's) glands in the female[MP]
Either of two small racemose glands that are located below the prostate and discharge a component of the seminal fluid into the urethra. They are homologous to the Bartholin's glands in the female[BTO].
Lobular organ the parenchyma of which consists of glandular acini which communicate the bulbar part of the urethra. Examples: There only two instances, right and left bulbo-urethral glands[FMA]
any of the small paired racemose (compound tubulo-alveolar) glands below the apex of the prostate in males, located posterolateral to the membranous portion of the urethra at the base of the penis, between the two layers of the fascia of the urogenital diaphragm, in the deep perineal pouch, and enclosed by transverse fibers of the sphincter urethrae membranaceae muscle; they secrete a clear fluid known as pre-ejaculate (Cowper's fluid), and are homologous to the greater vestibular (Bartholin's) glands in the female[MP].
The bulbourethral glands are compound tubulo-alveolar glands.
see comments for paraurethral gland - ncita placement may not be correct
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland.
Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]
A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]
the soft tissue that fills the cavities of bones
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx
the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region
tonsils on the left and right sides at the back of the throat. one of the mucosa-associated lymphoid tissues (MALT), located at the entrance to the upper respiratory and gastrointestinal tracts to protect the body from the entry of exogenous material through mucosal sites[WP].
tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches
A bone that is part of the metacarpal skeleton.
A cartilaginous ring that provides support for the arytenoid cartilages and forms the caudal part of the larynx.
Cartilaginous ring that provides support for the arytenoid cartilages. Its ventral part is bent posteriorly to form a V.[AAO]
The ringlike cartilage forming the caudal part of the larynx. [TFD][VHOG]
Any muscle that is part of a head[Automatically generated definition].
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Muscle organ which is a part of the neck. Examples: platysma, sternocleidomastoid, cricothyroid muscle.[FMA]
Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.
A muscle organ that is part of a perineum [Automatically generated definition].
In human anatomy, the trapezius is a large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted].
The pectoralis major is a thick, fan-shaped muscle, situated at the upper front of the chest wall. It makes up the bulk of the chest muscles in the male and lies under the breast in the female. Underneath the pectoralis major is the pectoralis minor, a thin, triangular muscle. [WP,unvetted].
The rectus abdominis muscle is a paired muscle running vertically on each side of the anterior wall of the human abdomen (and in some other animals). There are two parallel muscles, separated by a midline band of connective tissue called the linea alba (white line). It extends from the pubic symphysis/pubic crest inferiorly to the xiphisternum/xiphoid process and lower costal cartilages (5–7) superiorly. It is contained in the Rectus sheath. The rectus is usually crossed by three fibrous bands licked by the tendinous inscriptions. While the 'sixpack' is by far the most common configuration of the muscle bellies of the rectus, there exist rare anatomic variations which result in the appearance of eight ('eightpack'), ten, or—even rarer—asymmetrically arranged segments. All these variations are functionally equivalent. [WP,unvetted].
The supraspinatus is a relatively small muscle of the upper limb that takes its name from its origin from the supraspinous fossa superior to the spine of the scapula. It is one of the four rotator cuff muscles and also abducts the arm at the shoulder. The spine of the scapula separates the supraspinatus muscle from the infraspinatus muscle, which originates below the spine. [WP,unvetted].
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants.
The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG]
Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
middle limb segment of proximal segment of free upper limb
proximal segment of free upper limb middle limb segment
proximal segment of free upper limb zeugopod
zeugopod of proximal segment of free upper limb
distal portion of the hind limb, including tarsal region, metatarsal region and digits.
manual digit (phalangeal portion) plus soft tissue
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
Transudate contained in the lumen of lymphatic vessel[FMA]. Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system[WP].
the paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity
The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG]
Organ with organ cavity which connects the cavity of the middle ear to the cavity of the pharynx. Examples: There are only two pharyngotympanic tubes, the right and the left pharyngotympanic tubes.[FMA]
we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship
Furrow on the ventral surface of the otic capsule, and occasionally also the parasphenoid, that houses the Eustachian tube.[AAO]
The narrow channel connecting the nasopharynx and the middle ear. [TFD][VHOG]
tuba auditiva; tuba auditoria; tuba auditivea
Duct that carries bile from the liver to the small intestine.
Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG]
The path is as follows: Bile canaliculi → Canals of Hering → interlobular bile ducts → intrahepatic bile ducts → left and right hepatic ducts merge to form → common hepatic duct exits liver and joins → cystic duct (from gall bladder) forming → common bile duct → joins with pancreatic duct → forming ampulla of Vater → enters duodenum [WP]
A proximal tarsal bone resulting from fusion of intermedium and fibulare.
The talus is apparently derived from the fusion of three separate bones in the feet of primitive amphibians; the tibiale, articulating with tibia, the intermedium, between the bases of the tibia and fibula, and the fourth centrale, lying in the mid-part of the tarsus. These bones are still partially separate in modern amphibians, which therefore do not have a true talus. The talus forms a considerably more flexible joint in mammals than it does in reptiles. This reaches its greatest extent in artiodactyls, where the distal surface of the bone has a smooth keel to allow greater freedom of movement of the foot, and thus increase running speed
the triangular flat bone of the nasal septum
Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO]
Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO]
relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO]
relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO]
In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP]
The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO]
The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods.
Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO]
Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO]
relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO]
In some teleosts, the maxilla is located postero-ventral to the supramaxilla. Commonly, the articular process of the maxilla articulates with the autopalatine and ethmoidal region antero-medially. The maxilla is usually the largest bone in the upper jaw assemblage.[TAO]
distal segment of the fore limb, including carpal region, metacarpal region and digits.
like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton
The double layer of peritoneum that extends from the liver to the lesser curvature of the stomach and the start of the duodenum. [WP,unvetted].
exact part of and develops from relationships need to be established
A membranous extension of the peritoneum from the peritoneal layers covering the ventral and the dorsal surfaces of the stomach and the first part of the duodenum. The lesser omentum extends from the portal fissure of the liver to the diaphragm, where the layers separate to enclose the end of the esophagus. It also forms two ligaments, one associated with the liver, the hepatogastric ligament, and the other, the heptatoduodenal ligament, with the duodenum. [TFD][VHOG]
Parietal serous membrane which is continuous with the visceral pleura and is attached to the dome of the diaphragm.[FMA]
Visceral serous membrane which is continuous with the parietal pleura and is attached to the parenchyma of lobe of lung.[FMA]
Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura].
Cavity of serous sac surropunded by the pleura.[FMA]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
the EHDAA2 class is not quite equivalent. See http://purl.obolibrary.org/obo/uberon/tracker/86
Intercostal muscles are several groups of muscles that run between the ribs, and help form and move the chest wall. There are three principal layers; the external intercostal muscles, which aid in quiet and forced inhalation. They originate on ribs 1-11 and have their insertion on ribs 2-12. The external intercostals are responsible for the elevation of the ribs, and expanding the transverse dimensions of the thoracic cavity. Located around the ribs the internal intercostal muscles, which aid in forced expiration (quiet expiration is a passive process). They originate on ribs 2-12 and have their insertions on ribs 1-11. The internal intercostals are responsible for the depression of the ribs decreasing the transverse dimensions of the thoracic cavity. the innermost intercostal muscle, the deep layers of the internal intercostal muscles which are separated from them by the neurovascular bundle. Both the external and internal muscles are innervated by the intercostal nerves, and are provided by the intercostal arteries and intercostal veins. Their fibers run in opposite directions. [WP,unvetted].
The tranversus thoracis lies internal to the thoracic cage, anteriorly. It is a thin plane of muscular and tendinous fibers, situated upon the inner surface of the front wall of the chest. It is in the same layer as the subcostal muscles. It arises on either side from the lower third of the posterior surface of the body of the sternum, from the posterior surface of the xiphoid process, and from the sternal ends of the costal cartilages of the lower three or four true ribs. Its fibers diverge upward and lateralward, to be inserted by slips into the lower borders and inner surfaces of the costal cartilages of the second, third, fourth, fifth, and sixth ribs. The lowest fibers of this muscle are horizontal in their direction, and are continuous with those of the Transversus abdominis; the intermediate fibers are oblique, while the highest are almost vertical. This muscle varies in its attachments, not only in different subjects, but on opposite sides of the same subject. [WP,unvetted].
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
a double-walled sac containing the heart and the roots of the great vessels.
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Peritoneum that surrounds the heart.[AAO]
we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium
Parietal serous membrane which is part of the serous membrane.
Transudate contained in the pericardial cavity.[FMA]
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]
FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib
autonomic division of peripheral nervous system
autonomic part of peripheral nervous system
divisio autonomica systematis nervosi peripherici
pars autonomica systematis nervosi peripherici
the small, erectile body located at the anterior end of the vulva
Irregular bone that articulates with other vertebrae, or with one other vertebra and the skull or the sacrum[FMA]. All serially repeated ossified, cartilaginous, and ligamentous elements around the notochord (Schultze and Arratia, 1988)[ZFA].
Consider changing name to make distinction from inferred superclass 'vertebral element' clear
we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones
Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO]
Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO]
In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]
A vertebra that is located in the cervical region of the vertebral column.
In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery.
Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body.
Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J
section at the rear end of an animal's body; in general, the term refers to a distinct, flexible appendage to the torso[WP].
Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin
An organ system that protects the body from damage, forming the bounding layer of the organism and comprising the outer epithelial layer and any associated adnexa. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified].
it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment].
The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum
BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says "hippocampus" it means "hippocampal formation". In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures.
Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO]
The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592].
The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct
System responsible for the production and movement of bile[ZFIN:curator].
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].
A muscle organ that is part of a chest [Automatically generated definition].
anterolateral part of thorax muscle organ
muscle organ of anterior thoracic region
muscle organ of anterolateral part of thorax
A zone of skin that is part of an arm [Automatically generated definition].
proximal segment of free upper limb skin
skin of proximal segment of free upper limb
A bone that is part of a limb [Automatically generated definition].
the formal definition is very inclusive, and includes sesamoids
NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle
Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted].
The lateral hypothalamus or lateral hypothalamic area is a part of the hypothalamus. It is concerned with hunger. Damage to this area can cause reduced food intake. Stimulating the lateral hypothalamus causes a desire to eat, while stimulating the ventromedial hypothalamus causes a desire to stop eating. [WP,unvetted].
the thin boundary between the adenohypophysis and neurohypophysis of the pituitary that produces melanocyte stimulating hormone (MSH); this area is small or absent in mammalian adults
pars intermedia of anterior lobe of pituitary gland
pars intermedia lobi anterior hypophyseos
The pars tuberalis is part of the anterior lobe of the pituitary gland, and wraps the pituitary stalk in a highly vascularized sheath. [WP,unvetted].
pars tuberalis of anterior lobe of pituitary gland
the apical portion of the tubular structure extending from the hypothalamus to the posterior lobe of the pituitary gland
A short stalk connecting the pituitary with the brain. Axons of secretory cells in the floor of the diencephalon traverse the infundibulum and terminate in the neurohypophysis.[TAO]
infundibulum (lobus posterior) (glandula pituitaria)
infundibulum of posterior lobe of pituitary gland
A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO].
FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see http://en.wikipedia.org/wiki/Striatum#History. Check caudoputamen
The term area 17 of Brodmann (human) refers to a subdivision of the cytoarchitecturally defined occipital region of cerebral cortex in the human. Defined by the band of Gennari, which gives it the name striate (furrowed) area, it occupies the banks of the calcarine sulcus which are located in the cuneus and the lingual gyrus of the occipital lobe. Cytoarchitecturally it is bounded by the area 18 of Brodmann (human) which surrounds it ( Brodmann-1909 ). In the mouse ( Paxinos-2001 ) and the rat ( Swanson-1998 ) it is located on the dorsolateral surface of the cerebral hemisphere[BrainInfo].
We explicitly merge two FMA classes here, as BA17 is equivalent to V1
White matter that is part of a cerebral hemisphere.
sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere
The BTO class is inconsistent as it is part of the brain and spinal cord.
white matter structure of cerebral hemisphere
A nucleus of brain that is part of a ventral tegmental area.
ventral and anterior tegmental nucleus are synonyms in FMA, but we split these into seperate classes. This is consistent with MA, ABA and neuronames, which treat these as distinct (NN suggest the anterior is a rodent specific structure)
this is part of pons and brainstem in MA, but this leads to an inconsistency with ABA. We err on the side of safety, and exclude the relationship to the pons here.
One of two ganglionated neural networks which together form the enteric nervous system. The myenteric (Auerbach's) plexus is located between the longitudinal and circular muscle layers of the gut. Its neurons project to the circular muscle, to other myenteric ganglia, to submucosal ganglia, or directly to the epithelium, and play an important role in regulating and patterning gut motility.
plexus of unmyelinated nerve fibers and postganglionic autonomic cell bodies lying in the muscular coat of the esophagus, stomach and intestines that communicate with the submucosal, subserosal and enteric plexuses[MP][MP:0010801].
note that FMA uses Meissner's plexus as a synonym, rather than separate class
The inferior cervical ganglion is situated between the base of the transverse process of the last cervical vertebra and the neck of the first rib, on the medial side of the costocervical artery. Its form is irregular; it is larger in size than the middle cervical ganglion, and is frequently fused with the first thoracic ganglion. [WP,unvetted].
the group of neurons formed by the fusion of the inferior cervical and first thoracic ganglia
A blood vessel that is part of a choroid [Automatically generated definition].
cannot find singular in FMA, using Set class
the elongated cells of the crystalline lens of the eye
TODO - check plural vs singular. in FMA lens fiber is a cell - FMA:70950 Lens cell. Other ontologies don't appear to commit one way or another.
Fibres resembling a ribbon and arranged in very thin plates in the lens. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
(...) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG]
The postaxial bone of the proximal carpal region. Found in close approximation to the ulna, often in articulation[PHENOSCAPE:ad].
One of two element that constitute the basal row of carpals. It articulates with the ulna, radius, radiale, centrale (element Y), and carpal 5(4). This element originates from one condensation center or the fusion of two elements (ulnare and intermedium). Occasionally it may fuse to carpal 5(4), the radiale, or other elements.[AAO]
this bone is termed the triquetral bone in some mammalian taxa, notably humans
A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad]
The patella, also known as the knee cap or kneepan, is the largest sesamoid bone in the human body. The primary functional role of the patella is knee extension. The patella has convergently evolved in placental mammals and birds; marsupials have only rudimentary, non-ossified patellae. In more primitive tetrapods, including living amphibians and reptiles, the muscle tendons from the upper leg are attached directly to the tibia, and the patella is not present. See also: fabella.
The palatine glands form a continuous layer on its posterior surface and around the uvula. They are primarily mucous secreting glands, as opposed to serous or mixed secreting glands. [WP,unvetted].
Any of the mushroom-shaped papillae, which have a single taste bud at the tip, located mostly on the dorsal anterior portion of the tongue
The fungiform papillae are mushroom shaped e (projections) on the tongue. They are located on the top (dorsal) surface of the tongue, scattered throughout the filiform papilla but mainly at the tip and lateral margins of the tongue. They have taste buds on their superior (upper) surface which can distinguish the five tastes: sweet, sour, bitter, salty, and umami. They have a core of connective tissue. They are innervated by the seventh cranial nerve, more specifically via the submandibular ganglion, chorda tympani, and geniculate ganglion ascending to the solitary nucleus (the sensory component of the Vagus nerve in the brainstem). [WP,unvetted][Wikipedia:Fungiform_papilla].
In the mouse, Fungiform and palatal taste buds are innervated by the geniculate ganglion cells of the facial nerve[doi:10.1523/JNEUROSCI.5142-05.2006]
Uterine lining (endometrium) during a pregnancy, which forms the maternal part of the placenta. It is formed under the influence of progesterone and forms highly-characteristic cells.
The mucous secreting gland associated with the mucuous membrane lining the uterus.
the evaginations of the mucous membrane of the nasal cavity into the ethmoidal bony labyrinth, forming multiple small paranasal sinuses
Aanastomosis of dorsal carpal branch of the radial artery and the dorsal carpal branch of the ulnar artery near the back of the wrist. It is made up of the dorsal carpal branches of both the ulnar and radial arteries. It also anastomoses with the anterior interosseous artery and the posterior interosseous artery. The arch gives off three dorsal metacarpal arteries.
check FMA, singular. specific subtypes e.g. FMA:22761 first dorsal metacarpal artery
In human anatomy, the internal thoracic artery (ITA), previously known as the internal mammary artery (a name still common among surgeons), is an artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted].
The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries
Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061].
Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]
A blood vessel that drains from from an lower eyelid.
The vesical veins are veins in the pelvis that drain blood from the urinary bladder. The vesical veins receive blood from the vesical venous plexus and are tributaries of the internal iliac veins. [WP].
A muscle organ that is part of a anterior abdominal wall.
A bundle of muscles and tendons that is paired and runs more or less vertically. It extends throughout the lumbar, thoracic and cervical regions, and lies in the groove to the side of the vertebral column.
In human anatomy, the hamstring refers to one of the three posterior thigh muscles, or to the tendons that make up the borders of the space behind the knee. In modern anatomical contexts, however, they usually refer to the posterior thigh muscles, or the tendons of the semitendinosus, the semimembranosus and the biceps femoris. In quadrupeds, it refers to the single large tendon found behind the knee or comparable area. [WP,unvetted].
Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913].
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]
We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine.
The filiform papillae are thin, long 'V'-shaped cones that don't contain taste buds but are the most numerous. These papillae are mechanical and not involved in gustation covering most of the dorsum (upper surface). They are small and arranged in lines parallel to the V-shaped row of circumvallate papillae, except at the tip of the tongue where they are aligned transversely. Projecting from their apices are numerous filamentous processes, or secondary papillae. These are of a whitish tint, owing to the thickness and density of the epithelium of which they are composed. This epithelium has undergone a peculiar modification as the cells have become cornified and elongated into dense, imbricated, brush-like processes. They contain also a number of elastic fibers, which render them firmer and more elastic than the papillae of mucous membrane generally. The larger and longer papillae of this group are sometimes termed papillae conicae. Fungiform papillae are found dispersed throughout the filiform papillae. [WP,unvetted].
Any of the papillae located on the sides of the tongue
Taste-buds, the end-organs of the gustatory sense, are scattered over the mucous membrane of the mouth and tongue at irregular intervals. They occur especially in the sides of the vallate papillae. There is a localized area at the side of the base of the tongue, the foliate papillae, in which they are especially abundant. [WP,unvetted][Wikipedia:Foliate_papilla].
A mucosa that is part of a esophagus [Automatically generated definition].
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot
Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).
There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators]
The proximal free limb segment. Includes as parts the stylopod skeleton.
A commissure that connects the two cerebral hemispheres. Examples: anterior commissure, corpus callosum.
A composite structure of the brain stem, which is subdivided into the superior cerebellar peduncle of pons, the decussation of superior cerebellar peduncle and the superior cerebellar peduncle of midbrain (MM)[NIF, based on NN].
TODO - this requires work for making consistent with ABA, which strictly separates cerebellum from brainstem. in MA, cerebellar peduncle is part of both brainstem and cerebellar white matter.
The saphenous nerve (long or internal saphenous nerve) is the largest cutaneous branch of the femoral nerve. [WP,unvetted].
The more lateral of the two segments of the globus pallidus, abutting the putamen
The lateral globus pallidus (or external, GPe) receives a strong glutamatergic projection from the subthalamic nucleus. The two form a particular system: a coupled pacemaker. The axons of the external globus pallidum go essentially to the subthalamic nucleus. They go also to other elements of the basal ganglia system, the striatum, the substantia nigra pars reticulata, and the internal globus pallidus, where they release the neurotransmitter GABA. GPe is particular in comparison to the other elements of the set by the fact that it does not work as an output base of the basal ganglia (not sending axons to the thalamus) but as the main regulator of the basal ganglia system. It is sometimes used as a target for deep brain stimulation as a treatment for Parkinson's disease. [WP,unvetted][Wikipedia:Lateral_globus_pallidus].
The more medial segment of the globus pallidus.
The medial globus pallidus (or internal, GPi) is one of the output nuclei of the basal ganglia. The GABA-containing neurons send their axons to specific nuclei of the dorsal thalamus (VA and VL), to the centromedian complex and to the pedunculopontine complex. The efferent bundle is constituted first of the ansa and fasciculus lenticularis, then crosses the internal capsule as the Edinger's comb system then arrives at the laterosuperior corner of the subthalamic nucleus and constitutes the Forel's field H2, then H, and suddenly changes its direction to form H1 that goes to the inferior part of the thalamus. The distribution of axonal islands is widespread in the lateral region of the thalamus. The innervation of the central region is done by collaterals. [WP,unvetted][Wikipedia:Medial_globus_pallidus].
medial globus pallidus (entopeduncular nucleus)
the bone that is situated in the orbit on either side of the presphenoid; it generally forms a part of the sphenoid in the adult, and may be independent in the young
Endochondral ossification of the lateral sides of the braincase.[AAO]
Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO]
relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO]
relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO]
relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO]
relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO]
relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]
The main division of the lateral geniculate body; consists of two magnocellular layers [TA] (strata magnocellularia [TA]) and four parvocellular layers [TA] (strata parvocellularia [TA]) and serves as a processing station in the major pathway from the retina to the cerebral cortex, receiving fibers from the optic tract and giving rise to the geniculocalcarine radiation to the visual cortex in the occipital lobe.
nucleus dorsalis corporis geniculati lateralis
nucleus geniculatus lateralis pars dorsalis
dorsal nucleus of lateral geniculate body
dorsal part of the lateral geniculate complex
nucleus corporis geniculati lateralis, pars dorsalis
corpus geniculatum externum, nucleus accessorius
corpus geniculatum laterale, pars oralis
lateral geniculate complex, ventral part
lateral geniculate complex, ventral part (kolliker)
lateral geniculate nucleus, ventral part
nucleus corporis geniculati lateralis, pars ventralis
nucleus ventralis corporis geniculati lateralis
ventral part of the lateral geniculate complex
lateral geniculate complex, ventral part (Kvlliker)
nucleus geniculatus lateralis pars ventralis
ventral nucleus of lateral geniculate body
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
Bone tissue that has a regular parallel alignment of collagen into sheets (lamellae) and is mechanically strong.
histological classification, lamellar vs woven. Note that only FMA has woven
bone tissue that has a lattice-like or spongy structure; it is highly vascular and contains intercommunicating spaces filled with bone marrow
one of the two types of osseous tissue that form bones. Compared to compact bone, which is the other type of osseous tissue, it has a higher surface area but is less dense, softer, weaker, and less stiff. It typically occurs at the ends of long bones, proximal to joints and within the interior of vertebrae. Cancellous bone is highly vascular and frequently contains red bone marrow where hematopoiesis, which is the production of blood cells, occurs. The primary anatomical and functional unit of cancellous bone is the trabecula.
the medullary cavities of the bones where bone marrow is stored
Located in the main shaft (cortical bone) of a long bone (diaphysis) (consisting mostly of compact bone), the medullary cavity has walls composed of spongy bone (cancellous bone) and is lined with a thin, vascular membrane (endosteum)[Wikipedia:Bone_marrow_of_ovaryry_cavity]
not clear if the FMA intends to have two classes. MP:0000065: 'the medullary cavities of the bones.'. NCITA also has 'medullary bone'
The minute canals that pass the prostatic secretions to the urethra.
the vocal apparatus of the larynx, which includes the vocal cords and the opening between them
A small, slit-like aperture lying longitudinally on the floor of the pharynx.[AAO]
the dense, fibrous connective tissue joint between the tetrapod parietal bones and the frontal bone
A suture that connects the two frontal bones of the skull.
in humans, the frontal suture is a dense connective tissue structure that divides the two halves of the frontal bone of the skull in infants and children. It usually disappears by the age of six, with the two halves of the frontal bone being fused together. If it does not disappear it may be called a 'metopic suture' or 'sutura frontalis persistens. ' If the suture is not present at birth (craniosynostosis) it will cause a keel-shaped deformity of the skull called 'trigonocephaly. ' It is present in a fetal skull so that the skull can bend and is very elastic at the time of birth. The baby's head literally bends when coming out of the mother's womb. The space is filled as the child grows older. [WP,unvetted]
the dense, fibrous connective tissue joint between the parietal bones and the occipital bone
the dense, fibrous connective tissue joint between the tetrapod parietal bones
the branch of the internal iliac artery that supplies the uterus and the upper part of the vagina
one of the group of myocardial bundles which terminate in the chordae tendineae that attach to the cusps of the atrioventricular valves; each ventricle has an anterior and a posterior papillary muscle; the right ventricle sometimes has a septal papillary muscle
On the internal or parietal surface of the left ventricle in man and in mammals are two papillary muscles, which are almost identical and well developed.[well established][VHOG]
These muscles contract to tighten the chordae tendineae, which in turn prevent inversion. This occurs in response to pressure gradients. Instead they brace the valves against the high pressure, preventing regurgitation of ventricular blood back into the atrial cavities.[Wikipedia:Papillary_muscle]
Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd].
Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251]
The flat portion of the stirrup of the ear that fits in the oval window between the middle and inner ear.
Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa.
Anterior rounded projection of the pars acromialis of the scapula.[AAO]
relationship loss: part_of pars acromialis (AAO:0000752)[AAO]
a rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches
In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad]
The labyrinth is a system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. It is named by analogy with the mythical maze that imprisoned the Minotaur, because of its appearance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted].
we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear
the bony arch in vertebrates that extends along the side or front of the skull beneath the eye socket and is formed by the temporal process of the zygomatic bone and the zygomatic process of the temporal bone
The zygomatic arch is significant in evolutionary biology, as it is part of the structures derived from the ancestral single temporal fenestra of the synapsid ancestor of mammals.
The zygomatic process of the temporal arises by two roots: an anterior, directed inward in front of the mandibular fossa, where it expands to form the articular tubercle. a posterior, which runs backward above the external acoustic meatus and is continuous with the supramastoid crest. The upper border of the arch gives attachment to the temporal fascia; the lower border and medial surface give origin to the Masseter
The zygomatic arch is occasionally referred to as the zygoma, but this term usually refers to the zygomatic bone or occasionally the zygomatic process.
the oval opening on the medial wall of the tympanic cavity leading into the vestibule, close to the foot of the stapes
oval window of petrous part of temporal bone
the opening on the medial wall of the middle ear leading into the cochlea, closed in life by the secondary tympanic membrane; serves to regulate fluid pressure in the inner ear
round window of petrous part of temporal bone
The greater trochanter (great trochanter) of the femur is a large, irregular, quadrilateral eminence and a part of the skeletal system. It is directed a little lateralward and backward, and, in the adult, is about 1 cm lower than the head. Because the pelvic outlet in the female is larger than in the male, there is a greater distance between the greater trochanters in the female. It has two surfaces and four borders. [WP,unvetted].
The lesser trochanter (small trochanter) of the femur is a conical eminence, which varies in size in different subjects [WP,unvetted].
The artery which parallels the spiral ganglion in the root of the spiral lamina of the modiolus, serving the ganglion and the cochlear duct and its contents.
An epithelium that is part of a iris [Automatically generated definition].
A lymph node that is part of an abdomen [Automatically generated definition].
the visceral glands that are associated with the branches of the celiac artery, including the gastric, hepatic, and pancreaticolienal (splenic) lymph nodes
The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.
In humans, the anterior fontanelle (bregmatic fontanelle, frontal fontanelle) is the largest, and is placed at the junction of the sagittal suture, coronal suture, and frontal suture; it is lozenge-shaped, and measures about 4 cm in its antero-posterior and 2.5 cm in its transverse diameter. The fontanelle allows the skull to deform during birth to ease its passage through the birth canal and for expansion of the brain after birth. While the posterior and lateral fontanelles are obliterated by about six months after birth, the anterior is not completely closed until about the middle of the second year. Full ossification starts in the late twenties and finishes before the age of 50 . [WP,unvetted].
TAO:0001739 anterior cranial fontanel is 'Fontanel that is located between the contralateral frontals and anterior to the epiphyseal bar'
the supporting bundles of muscular fibers lining the walls of the ventricles of the heart
The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented
Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea.
A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID].
maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
the thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints
A hyaline cartilage plate in the metaphysis at each end of a long bone. The plate is found in children and adolescents; in adults, who have stopped growing, the plate is replaced by an epiphyseal line.
consider splitting this class into the epiphyseal plates of long bones and vertebrae
The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof.
The skull base is formed from a series of cartilages either side of, and rostral to, the notochord, whose tip lies just caudal to the pituitary gland. It is closely associated with the sensory capsules, which partially or completely sur- round the olfactory epithelium, the eye, and the inner ear[PMID:11523816]
the crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane)
Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia
In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG]
The layer of the statoconial membrane that is composed of otoliths
The submandibular lymph nodes (submaxillary glands in older texts), three to six in number, are placed beneath the body of the mandible in the submaxillary triangle, and rest on the superficial surface of the submaxillary salivary gland. One gland, the middle gland of Stahr, which lies on the external maxillary artery as it turns over the mandible, is the most constant of the series; small lymph glands are sometimes found on the deep surface of the submaxillary salivary glands. The afferents of the submaxillary glands drain the medial palpebral commissure, the cheek, the side of the nose, the upper lip, the lateral part of the lower lip, the gums, and the anterior part of the margin of the tongue. Efferent vessels from the facial and submental glands also enter the submaxillary glands. Their efferent vessels pass to the superior deep cervical glands. [WP,unvetted].
Connective tissue composed of elastic fibers.
The middle layer of an artery or vein. [WP,unvetted].
May be composed of smooth muscle and elastic tissue
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
A lymph node that is part of a mediastinum. Each consists of several lymph node groups, especially along the trachea (5 groups), along the esophagus and between the lung and the diaphragm. In the mediastinal lymph nodes arises lymphatic ducts, which draines the lymph to the left subclavian vein (to the venous angle in the confluence of the subclavian and deep jugular veins). The mediastinal lymph nodes along the esophagus are in tight connection with the abdominal lymph nodes along the esophagus and the stomach. That fact facilitates spreading of tumors cells through these lymphatics in cases of cancers of the stomach and particularly of the esophagus. Through the mediastinum, the main lymphatic drainage from the abdominal organs goes via the thoracic duct (ductus thoracicus), which drains majority of the lymph from the abdomen to the above mentioned left venous angle.
The lymph nodes located along the brachial vein that receive drainage from most of the free upper limb and send efferent vessels to the central axillary lymph nodes.
The lumbar lymph nodes (paraaortic nodes) are a group of lymph nodes residing in the lumbar region. They consist of the following groups: right and left lateral aortic lymph nodes preaortic lymph nodes retroaortic lymph nodes (or 'postaortic')
A lymph node that is part of a pancreas [Automatically generated definition].
A lymph node located in the sacral region.
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition
FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
an organ that functions as a secretory or excretory organ
An outgrowth on the lateral trunk of the embryo that develops into a paired fin. The fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Embryonic surface structure that develops into a paired fin.[ZFA]
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node.
Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG]
Fin that is one of a pair located ventrally on the organism.
Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians.
this term potentially applicable across multiple metazoa - see also the subclass 'pharyngeal arch derived gill'
Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt]
A gonad with both testicular and ovarian aspects[WP].
The cells of the hatching gland contain enzymes responsible for solubilization of the egg chorion, facilitating the hatching process[GO]. A transversely oriented set of cells located deep to the EVL on the pericardial membrane, especially prominent during pharyngula period because of the brightly refractile cytoplasmic granules (containing hatching enzymes) of the principal cells of the gland.
A transversely oriented set of cells located deep to the EVL on the pericardial membrane, especially prominent during pharyngula period because of the brightly refractile cytoplasmic granules (containing hatching enzymes) of the principal cells of the gland. Kimmel et al, 1995.[TAO]
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
A line of neuroblasts along the sides of fish and amphibia that detect vibrations and pressure changes.
A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]
Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO]
relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO]
The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG]
The thickend rim of the blastoderm evident during late blastula and gastrula stages[FishBase]. Embryonic structure which is a uniform thickened annulus at the blastoderm margin, consisting of two layers in addition to the EVL, the epiblast and the hypoblast. The germ ring is formed by the involution of the blastoderm back upon itself[ZFA]
TODO - check timing of appearance and disappearance - check relationship with primitive streak. he blastopore lips in amphibians appear to have the equivalent function of the germ ring in zebrafish (ES)
Embryonic structure that forms as a thickened annulus at the blastoderm rim. The germ ring is thickened because it is the involuting margin of the blastoderm[ZFIN:ZDB-PUB-961014-576].
A small rigid plate that grows out of an animal's skin to provide protection. In lepidopteran (butterfly and moth) species, scales are plates on the surface of the insect wing, and provide coloration. Scales are quite common and have evolved multiple times with varying structure and function.
currently defined in a very inclusive fashion - may be obsoleted and replaced by more specific classes in future versions. The TAO, VSAO amd ZFA classes by this name are classified as 'dermal scales'. Can also be classified by composition - e.g. pangolin keratin scales.
Postcranial axial skeleton that is unpaired and located on the sagittal plane of the organism.
Mistakenly placed in uberon, should remain domain of TAO for now
A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion
Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
digit (phalangeal portion) plus soft tissue
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
to avoid confusion, we include neurogenic placode as a subclass. Do not merge.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this.
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
TODO discriminate between stages and organisms
Whole organism that is premetamorphic or a very immature individual.[TAO]
The Anterior trigeminothalamic tract (or ventral trigeminothalamic tract) serves as pain, temperature, and light touch pathway from the face, head and neck. It receives input from trigeminal nerve, facial nerve, glossopharyngeal nerve and vagus nerve. It receives discriminative tactile and pressure input from the contralateral principal sensory nucleus of CN V, which terminates in the ventral posteromedial nucleus of the thalamus. It then ascends to the contralateral sensory cortex via three neurons .
The largest and most prominent of the cell groups of the medial longitudinal fasciculus
interstitial nucleus of medial longitudinal fasciculus
interstitial nucleus of medial longitudinal fasciculus (Crosby)
interstitial nucleus of the medial longitudinal fascicle (Boyce 1895)
interstitial nucleus of the medial longitudinal fasciculus
nucleus of the posterior commissure (Kvlliker)
White matter tract containing axons arising in the vestibular ganglion primarily projecting to the ipsilateral cerebellum via the inferior cerebellar peduncle (Heimer, L. The Human Brain, 2nd ed., 1995, pg 370).
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
A multi-tissue structure that is part of a superior colliculus.
obsolete regional part of superior colliculus
The portion of the hypothalamus located generally internal to the region of the infundibulum.
See notes for pars intermedia of adenohypophysis.
Brain structure that lies perpendicular to the longitudinal axis of the embryonic neural tube, is continuous with the rostral hypothalamic proliferation and whose most lateral extent is deflected dorsally within the inferior lobe.[TAO]
In humans it contains the following nuclei: dorsal nucleus [TA] (nucleus dorsalis hypothalami [TA]), parts of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), arcuate nucleus [TA] (nucleus arcuatus [TA]), posterior periventricular nucleus [TA] (nucleus periventricularis posterior [TA]), retrochiasmatic area [TA] (area retrochiasmatica [TA]), lateral tuberal nuclei [TA] (nuclei tuberales laterales [TA]), and ventromedial nucleus [TA] (nucleus ventromedialis hypothalami
rostral and caudal linear nuclei of the raphe
The mesocorticolimbic dopamine (DA) system plays important roles in reward, motivation, learning, memory, and movement. This system arises from the A10 region, comprising the ventral tegmental area and three adjacent midline nuclei (caudal linear nucleus, interfascicular nucleus, and rostral linear nucleus of the raphe)[PMID:21653852]
The reticular formation is a series of brain nuclei located in the medulla oblongata
ZFA:0000421 is part of the the medulla oblongata, so it is placed here, rather than with the generic term
reticular formation of medulla oblongata
reticular formation of medulla oblonmgata
Part of temporal lobe overlaying the insular cortex
The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube
cavity of ventricular system of neuraxis
The superior frontal sulcus is a sulcus between the superior frontal gyrus and the middle frontal gyrus. [WP,unvetted].
central cortex of the inferior colliculus
central nucleus of the inferior colliculus
nucleus centralis (colliculi inferioris)
Small distinct nucleus in the pretectum of mammals involved in the pupillary light reflect. In rats, it is an olive shaped (anterior) nucleus lying ventral to the brachium of the superior colliculus (Paxinos, The rat nervous system, 2nd ed, 1995, pg. 862). Physiologically, it is identified by neurons sensitive to luminance changes.
nucleus olivaris colliculi superioris (Fuse)
nucleus olivaris corporis quadrigemini anterioris
Ventral subdivision of the pons which consists of the massive pontine pertuberance on pontine ventral surface.
external cortex of the inferior colliculus
external nucleus of the inferior colliculus
The reticular formation is a part of the brain that is involved in actions such as awaking/sleeping cycle, and filtering incoming stimuli to discriminate irrelevant background stimuli. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. [WP,unvetted].
A regional part of brain that is part of a inferior olivary complex [Automatically generated definition].
obsolete regional part of inferior olivary complex
Anterior component of the temporal lobe (rostral boundary) extends caudally to the entorhinal cortex. The medial and lateral boundaries are the medial aspect of the temporal lobe and the superior or inferior temporal sulci, respectively (Christine Fennema-Notestine).
dorsal cortex of the inferior colliculus
nucleus pericentralis (colliculi inferioris)
pericentral nucleus of the inferior colliculus
pericentral nucleus of inferior colliculus
A regional part of brain that is part of a medullary reticular formation [Automatically generated definition].
segment of medullary reticular formation
obsolete regional part of medullary reticular formation
Bundle of fibers that passes over the medial geniculate nucleus (in humans) to reach the superior colliculus. Contains afferents from the retina.
Component of the parietal lobe. The appearance and disappearance of the central sulcus were the rostral and caudal boundaries of the postcentral gyrus respectively. The medial and lateral boundaries were the lateral bank of the precentral gyrus and the lateral fissure and/or the medial bank of the superior parietal gyrus respectively (Christine Fennema-Notestine).
A commissure that is part of a superior colliculus [Automatically generated definition].
anterior corpus quadrigeminum commissure
commissure of anterior corpus quadrigeminum
A regional part of brain that is part of a vestibular nuclear complex [Automatically generated definition].
obsolete regional part of vestibular nuclear complex
tractus tegmentalis centralis (mesencephali)
The calcarine fissure is an anatomical landmark located at the caudal end of the medial surface of the brain. [WP,unvetted].
Regional part of superior cerebellar peduncle located in the caudal midbrain, at the level of the inferior colliculus, consisting of a large bundle of fibers crossing the midline. It contains fibers projecting from the deep cerebellar nucleus to the midbrain and thalamus through the superior cerebellar peduncle (MM). The decussation of superior cerebellar peduncle is the portion of the superior cerebellar peduncle which crosses into the midbrain. [WP,unvetted].
decussatio pedunculorum cerebellarium superiorum
decussation of superior cerebellar peduncles
superior cerebellar peduncle decussation
decussatio crurorum cerebello-cerebralium
decussation of the superior cerebellar peduncle
decussation of the superior cerebellar peduncle (Wernekinck)
decussation of superior cerebellar peduncle
Part of the corticospinal tract located in the spinal cord, formed as 75 to 90% of the corticospinal fibers cross to the opposite side of the brainstem in the pyramidal decussation. This tract descends the length of the spinal cord in the lateral white column (Adapted from Brain Info)
lateral corticospinal tract of the medulla
tractus corticospinalis (pyramidalis) lateralis
Spinal nucleus of the trigeminal oral part
nucleus oralis tractus spinalis nervi trigemini
nucleus spinalis nervi trigemini, pars oralis
oral part of the spinal trigeminal nucleus
spinal nucleus of the trigeminal, oral part
Fibers interconnecting the cerebellum and vestibular nuclei, traveling medial to the restiform body (inferior cerebellar peduncle) (Nolte, The Human Brain, 6th ed., pg 497)
The dentatothalamic tract (or dentatorubrothalamic tract) is a tract which connects the dentate nucleus and the thalamus. [WP,unvetted].
The inferior or orbital surface of the frontal lobe is concave, and rests on the orbital plate of the frontal bone. It is divided into four orbital gyri by a well-marked H-shaped orbital sulcus
Part of thalamus receiving primary somatic sensory information via the medial lemniscal pathway that projects to the primary somatosensory cortex (adapted from Paxinos, The Rat Nervous System, 2nd Ed, Academic Press, 1995).
ventral posterior complex of the thalamus
The principal sensory nucleus (or chief sensory nucleus of V) is a group of second order neurons which have cell bodies in the dorsal Pons. It receives information about discriminative sensation and light touch of the face as well as conscious proprioception of the jaw via first order neurons of CN V. Most of the sensory information crosses the midline and travels to the contralateral ventral posteriomedial (VPM) of the thalamus via the Ventral Trigeminothalamic Tract, but information of the oral cavity travels to the ipsilateral Ventral Posteriomedial (VPM) of the thalamus via the Dorsal Trigeminothalamic Tract. [WP,unvetted].
principal sensory nucleus of trigeminal nerve
trigeminal nerve superior sensory nucleus
nucleus sensibilis superior nervi trigemini
nucleus sensorius principalis nervi trigemini
nucleus sensorius superior nervi trigemini
principal sensory nucleus of the trigeminal
principal sensory nucleus of the trigeminal nerve
GO has pontine nucleus as a child of trigeminal sensory nucleus, WP says this is a synonym, but we have a separate class for this - UBERON:0002151
Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem
A small paired band that passes around the splenium of the corpus callosum from the lateral longitudinal stria to the dentate gyrus[Biology-Online]. A posterior and upward extension of the dentate gyrus, forming a transitional area between the dentate gyrus and the indusium griseum[BTO].
TODO - existing definitions, synonyms and relationships in existing AOs seem contradictory; to be resolved. We take the dentate gyrus relationship from BTO, and it is also implied by the FMA synonym. However, FMA says archiortex (embryonic archicortex corresponds to the cortex of the dentate gyrus and hippocampus) and NIF says limbic lobe (which is more general than hippocampus). ABA xref made on basis of BTO related synonym
the small wedge shaped nucleus interposed between the dentate and fastigial nuclei; it receives axons from Purkinje cells of the intermediate area of the cerebral hemispheres and most of its efferent connections travel via the superior cerebellar peduncle
lateral interpositus (emboliform) nucleus
The paraterminal gyrus (subcallosal gyrus, peduncle of the corpus callosum) is a narrow lamina on the medial surface of the hemisphere in front of the lamina terminalis, behind the parolfactory area, and below the rostrum of the corpus callosum. It is continuous around the genu of the corpus callosum with the supracallosal gyrus. [WP,unvetted].
The lateral lemniscus is a tract of axons in the brainstem that carries information about sound from the cochlear nucleus to various brainstem nuclei and ultimately the contralateral inferior colliculus of the midbrain. Three distinct, primarily inhibitory, cellular groups are located interspersed within these fibers, and are thus named the nuclei of the lateral lemniscus. [WP,unvetted].
nucleus of the lateral lemniscus, ventral part
ventral nucleus of the lateral lemniscus
nucleus lemnisci lateralis pars ventralis
nucleus of the lateral lemniscus ventral part
The ventrolateral lip of the precentral gyrus, which overlies the insula and is bounded by the lateral fissure (Brain Info).
A cluster of ➞neurites that is part of a ➞nervous system and forms a network of dendrites and axons where ➞synapses are present and in which neuronal somata do not occur.
Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex.
dorsal part of ventral lateral posterior nucleus (jones)
nucleus lateralis intermedius mediodorsalis situs dorsalis
nucleus ventralis lateralis, pars caudalis
ventral lateral thalamic nucleus, caudal part
caudal part of the ventral lateral nucleus
The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted].
WP says 'The CN is located at the dorso-lateral side of the brainstem, spanning the junction of the pons and medulla.'. MA places this in pons, other sources the medulla
One of two nuclei comprising the interpositus cerebellar nuclear complex of the deep cerebellar nuclei.
The globose nucleus is one of the deep cerebellar nuclei. It is located medial to the emboliform nucleus and lateral to the fastigial nucleus. This nucleus contains primarily large and small multipolar neurons. The globose nucleus and emboliform nucleus are occasionally referred to collectively as the interposed nucleus. [WP,unvetted][Wikipedia:Globose_nucleus].
It is recognized in human cerebellum but is not distinguishable in all mammalian species
nucleus interpositus posterior cerebelli
nucleus ventralis lateralis thalami, pars medialis
medial part of the ventral lateral nucleus
nucleus ventralis lateralis, pars medialis
inferior decussation (Forel's decussation)
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. Regions of brain across multiple species are contained within this category.
nucleus dorsointermedius externus magnocellularis (hassler)
nucleus lateralis intermedius mediodorsalis situs postremus
nucleus ventralis lateralis thalami, pars postrema
posterodorsal part of ventral lateral posterior nucleus (jones)
nucleus ventralis lateralis, pars postrema
pars postrema of the ventral lateral nucleus
ventrolateral posterior thalamic nucleus
pars postrema of ventral lateral nucleus
A regional part of brain that is part of a cerebral cortex [Automatically generated definition].
obsolete regional part of cerebral cortex
Part of hypothalamus consisting of hollow eminence of gray matter situated between the mammilary bodies and the optic chiasm visible on the basal surface of the brain (adapted from Wikipedia)
A regional part of brain that is part of a cochlear nuclear complex [Automatically generated definition].
obsolete regional part of cochlear nuclear complex
The preoptic periventricular nucleus is located along the midline and is medial to the medial preoptic nucleus.[WP,unvetted].
preoptic periventricular hypothalamic nucleus
Periventricular hypothalamic nucleus, preoptic part
dorsal periventricular hypothalamic nucleus
nucleus periventricularis hypothalami, pars dorsalis
periventricular nucleus, anterior portion
Synonym for macrodissected adult human tegmentum (Vicq d'Azyr, 1784; Swanson, 2000); pp. 555-556. Later used thus by for example His (1893b, p. 178), Herrick (1915, p. 160), Strong & Elwyn (1943, p. 17), Carpenter (1976, p. 367), Williams & Warwick (1980, p. 935).
Neuronames includes the substantia nigra, crus cerebri and midbrain tegmentum as substructures of the cerebral peduncle; the mouse atlases only include the crus cerebri as the cerebral peduncle (MM)
Component of the inferior frontal gyrus.defined as the first gyrus from the precentral gyrus.the remainder of the inferior frontal gyrus once the pars opercularis and triangularis have been defined (Christine Fennema-Notestine)., NeuroNames
pars orbitalis gyri frontalis inferioris
The median preoptic nucleus is located along the midline in a position significantly dorsal to the other 3 preoptic nuclei, at least in the macaca fascicularis brain. It wraps around the top (dorsal), front, and bottom (ventral) surfaces of the anterior commissure. The median preoptic nucleus generates thirst. Drinking decreases noradrenaline release in the median preoptic nucleus.
periventricular nucleus, preventricular portion
Largest part of the caudate nucleus lying lateral to and protruding into the anterior of the lateral ventricle
Narrowest part of the caudate nucleus, roughtly defined as that portion that curves ventrally from the body of the caudate nucleus, following the temporal horn of the lateral ventricle
Component of the inferior frontal gyrus.defined as the second gyrus from the precentral gyrus (Christine Fennema-Notestine).
pars triangularis gyri frontalis inferioris
inferior frontal gyrus, pars triangularis
triangular part of inferior frontal gyrus
Part of caudate nucleus lying just dorsal to the thalamus
The cerebral crus is the anterior portion of the cerebral peduncle which contains the motor tracts, the plural of which is cerebral crura. In some older texts, it is used as a synonym for the entire cerebral peduncle, not just the anterior portion of it. [WP,unvetted].
medial subdivision of medial mammillary nucleus
medial part of the medial mammillary nucleus
nucleus corporis mamillaris medialis, pars medialis
nucleus medialis corpus mamillaris (Shantha)
medial part of medial mammillary nucleus
Nucleus located in the pontine tegmentum containing cells that give rise to motor innervation of the jaw through the trigeminal nerve. It receives both crossed and uncrossed fibers from the cerebral cortex (Heimer, L. The Human Brain and Spinal Cord, 2nd ed., 1996, pg 248).
this in ZFA this is part of the medulla; pons is a dubious structure for zebrafish
a loose heterogeneous collection of cells in the anterior hypothalamus, continuous rostrally with the medial and lateral preoptic areas and caudally with the tuber cinereum
anterior hypothalamic area anterior part
anterior hypothalamic area, anterior part
A multi-tissue structure that is part of a midbrain tegmentum.
obsolete regional part of midbrain tegmentum
nucleus pulvinaris thalami, pars lateralis
The ventral anterior nucleus is a nucleus of the thalamus. [WP,unvetted].
ventral anterior nucleus of the thalamus
nucleus pulvinaris thalami, pars medialis
Part of the reticular formation located in the midbrain tegmentum
formatio reticularis tegmenti mesencephali
White matter tract that originates from the cuneate and external cuneate nuclei. It relays ascending spinal fibers in the dorsal funiculus and conveys information from forelimbs to the cerebellum.
Part of cuneate fasciculus found in the medulla
TODO - change definition to be the *whole* of the CF in the MO. isa parentage to fasciculus of brain should be inferred
nucleus pulvinaris oromedialis (Hassler)
The sensory decussation or decussation of the lemniscus is a decussation or cross over of axons from the gracile nucleus and cuneate nucleus. The fibres of this decussation are called the internal arcuate fibres and are found at the superior aspect of the closed medulla superior to the motor decussation. It is part of the second neuron in the Posterior column-medial lemniscus pathway. [WP,unvetted].
nucleus medialis dorsalis paralamellaris (Hassler)
nucleus medialis dorsalis, pars densocellularis
densocellular part of the medial dorsal nucleus
densocellular part of medial dorsal nucleus
Part of dorsal longitudinal fasciculus located in the medulla
medulla posterior longitudinal fasciculus
posterior longitudinal fasciculus of medulla
dorsal longitudinal fasciculus of the medulla
fasciculus longitudinalis dorsalis (myelencephali)
dorsal longitudinal fasciculus of medulla
dorsomedial thalamic nucleus, magnocellular part
magnocellular nucleus of medial dorsal nucleus of thalamus
magnocellular part of dorsomedial nucleus
magnocellular part of mediodorsal nucleus
nucleus medialis dorsalis, pars magnocellularis
pars magnocellularis nuclei mediodorsalis thalami
magnocellular part of the medial dorsal nucleus
magnocellular part of medial dorsal nucleus
Part of Lissauer's tract located in the medulla
resolve distinction between Lissauer's tract and the medullary component
dorsomedial thalamic nucleus, paralaminar part
mediodorsal thalamic nucleus, paralaminar part
nucleus medialis dorsalis caudalis (hassler)
nucleus medialis dorsalis thalami, pars multiformis
nucleus medialis dorsalis, pars multiformis
nucleus medialis dorsalis, pars paralaminaris
paralaminar part of medial dorsal nucleus of thalamus
pars paralaminaris nuclei mediodorsalis thalami
pars paralaminaris of medial dorsal nucleus of thalamus
mediodorsal thalamic nucleus paralaminar part
paralaminar part of the medial dorsal nucleus
paralaminar part of medial dorsal nucleus
Part of the lateral ventricle that extends anteriorly into the frontal lobes, bordered by the head of the caudate nucleus on the lateral side (Adapted from Heimer, 1996)
Part of gracile fasiculus located in the medulla
fasciculus dorsolateralis gracilis (Golli)
dorsomedial thalamic nucleus, parvicellular part
lateral nucleus of medial dorsal nucleus of thalamus
mediodorsal thalamic nucleus, pars fasciculosa
nucleus medialis dorsalis fasciculosis (hassler)
nucleus medialis dorsalis nucleus fasciculosis (hassler)
nucleus medialis dorsalis, pars parvicellularis
pars parvocellularis lateralis nuclei mediodorsalis thalami
pars principalis nuclei ventralis anterior thalami
parvicellular part of dorsomedial nucleus
parvocellular nucleus of medial dorsal nucleus of thalamus
principal division of ventral anterior nucleus of thalamus
nucleus medialis dorsalis nucleus fasciculosus (Hassler)
nucleus medialis dorsalis, pars parvocellularis
parvicellular part of the medial dorsal nucleus
parvicellular part of medial dorsal nucleus
Part of lateral ventricle consisting of the central portion that lies dorsally, bounded by the thalamus on the ventral side (Adapted from Heimer, 1996)
The body of lateral ventricle (cella) extends from the interventricular foramen to the splenium of the corpus callosum. It is an irregularly curved cavity, triangular on transverse section, with a roof, a floor, and a medial wall. The roof is formed by the under surface of the corpus callosum; the floor by the following parts, enumerated in their order of position, from before backward: the caudate nucleus of the corpus striatum, the stria terminalis and the terminal vein, the lateral portion of the upper surface of the thalamus, the choroid plexus, and the lateral part of the fornix; the medial wall is the posterior part of the septum pellucidum, which separates it from the opposite ventricle. [WP,unvetted][Wikipedia:Body_of_lateral_ventricle].
Is located ventral to the basal nucleus and has three subdivisions: the periamygdaloid cortex, the medial division, and the sulcal division.
The posterior parahippocampal gyrus is a portion of the parahippocampal gyrus. It can show deterioration in Alzheimer's disease.
parahippocampal gyrus, posterior division
Part of medial lemniscus located within the midbrain
The superior medullary velum (anterior medullary velum, valve of Vieussens) is a thin, transparent of white substance, which stretches between the superior cerebellar peduncles; on the dorsal surface of its lower half the folia and lingula are prolonged. It forms, together with the superior cerebellar peduncle, the roof of the upper part of the fourth ventricle; it is narrow above, where it passes beneath the inferior colliculi, and broader below, where it is continuous with the white substance of the superior vermis. A slightly elevated ridge, the fraenulum veli, descends upon its upper part from between the inferior colliculi, and on either side of this the trochlear nerve emerges. Blood is supplied by branches from the superior cerebellar artery. [WP,unvetted].
A medial longitudinal fasciculus that is part of a midbrain [Automatically generated definition].
fasciculus longitudinalis medialis (mesencephali)
medial longitudinal fasciculus of the midbrain
medial longitudinal fasciculus of midbrain
Component of the frontal lobe, lateral aspect. The rostral boundary is the first appearance of the superior frontal sulcus whereas the caudal boundary is the midpoint of the paracentral sulcus on the "inflated" surface. The medial and lateral boundaries are the medial aspect of the frontal lobe and the superior frontal sulcus respectively (Christine Fennema-Notestine).
Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone).
Any of the groups of neural nuclei situated in the septal region which have afferent and cholinergic efferent connections with a variety of forebrain and brainstem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdala.
The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens. In the 1950s, Olds & Milner showed that rats with electrodes implanted in this area will self-stimulate repeatedly in order to experience a euphoric feeling (i.e. press a bar to receive electrical current that will stimulate the neurons). [WP,unvetted][Wikipedia:Septal_nuclei].
in NIFSTD this is the mereological sum of the individual complexes - in MA it is the superclass
lateral subdivision of medial mammillary nucleus
lateral part of the medial mammillary nucleus
nucleus corporis mamillaris medialis, pars lateralis
nucleus intercalatus corporis mammillaris
lateral part of medial mammillary nucleus
The supracallosal gyrus (indusium griseum; gyrus epicallosus) consists of a thin layer of grey matter in contact with the dorsal surface of the corpus callosum and continuous laterally with the grey matter of the cingulate gyrus. It contains two longitudinally directed strands of fibers termed respectively the medial and lateral longitudinal striae. The supracallosal gyrus is prolonged around the splenium of the corpus callosum as a delicate lamina, the fasciola cinerea, which is continuous below with the fascia dentata hippocampi. [WP,unvetted].
mesencephalic tract of the trigeminal nerve
tractus mesencephalicus nervi trigeminalis
Regional part of the septal nuclei, lying dorsal and slightly lateral to the medial septal nucleus. The lateral septum receives the bulk of projections of areas projecting to the septal nuclei (Adapted from Brodal, 1981).
Initial segment of the occulomotor nerve as it leaves the midbrain.
todo - determine pattern for central part of nerve vs fibers vs root
anterior horizontal limb of lateral fissure
anterior horizontal ramus of lateral fissure
anterior ramus of lateral cerebral sulcus
ramus anterior horizontalis sulcus lateralis
anterior horizontal limb of lateral sulcus
anterior ascending limb of lateral fissure
anterior ascending ramus of lateral sulcus
ascending ramus of lateral cerebral sulcus
anterior ascending limb of the lateral fissure
ramus anterior ascendens fissurae lateralis
ramus ascendens sulci cerebri lateralis (Sylvii)
anterior ascending limb of lateral sulcus
The vestibular nuclei are the cranial nuclei for the vestibular nerve. [WP,unvetted].
In TA they are grouped in both the pons and medulla; WP+MA says the SVN is in the pons, and GO includes VNC development under pons development, but this is not supported by ABA. Todo - check with NIF.
nuclei vestibulares in medulla oblongata
The ventral supraoptic decussation is the crossover point for signals from the left and right eye, en route respectively to the right and left sides of the visual cortex. Occupying the posterior part of the commissure of the optic chiasma is a strand of fibers, the Ventral supraoptic decussation (commissure of Gudden, Gudden's inferior commissure), which is not derived from the optic nerves; it forms a connecting link between the medial geniculate bodies. [WP,unvetted].
ventral supraoptic commissure (of Meynert)
supraoptic commissures, ventral (Gudden)
ventral supraoptic decussation of gudden
A regional part of brain that is part of a medullary raphe nuclear complex [Automatically generated definition].
segment of medullary raphe nuclear complex
obsolete regional part of medullary raphe nuclear complex
A regional part of brain that is part of a medulla oblongata [Automatically generated definition].
obsolete regional part of medulla oblongata
A regional part of brain that is part of a metencephalon [Automatically generated definition].
Nucleus located beneath the floor of the 4th ventricle in the pontine tegmentum, containing motor neurons innervating the lateral rectus muscle of the eye (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 533)
Hindbrain motor nucleus which is the origin of motor axons of cranial nerve VI. From Neuroanatomy of the Zebrafish Brain.[TAO]
part of medulla oblongata in ABA and ZFA; part of pons in MA and pontine tegmentum in NIF; note that pons/medulla are spatially disjoint in ABA.
In the human brain, the rhinencephalon appears as a longitudinal elevation, with a corresponding internal furrow, on the under surface of the hemisphere close to the lamina terminalis; it is separated from the lateral surface of the hemisphere by a furrow, the external rhinal fissure (or rhinal sulcus), and is continuous behind with that part of the hemisphere, which will ultimately form the anterior end of the temporal lobe. [WP,unvetted].
The raphe obscurus projects to the cerebellar lobes VI and VII and to crus II along with the nucleus raphe pontis . This so called obscure nucleus has also been implicated in the modulation of the hypoglossal nerve. It has been observed that the ablation of this nucleus causes a change in the firing pattern in the XII nerve . In addition, the raphe obscurus mediates expiration via the inhibitory effect of serotonin and depresses periodic synaptic potentials . It has also been shown that this nucleus stimulates gastrointestinal motor function; microinjections of 5-HT into the n.r. obscurus increase gastric movement . [WP,unvetted].
Part of inferior parietal lobule formed by the cortex surrounding the upturned end of the superior temporal sulcus (Nolte, The Human Brain, 6th ed, 2009, pg 659)
anteromedial part of ventral lateral posterior nucleus (jones)
nucleus lateralis intermedius mediodorsalis situs ventralis medialis
nucleus ventralis oralis, pars posterior (dewulf)
nucleus ventrooralis internus, superior part
nucleus ventro-oralis internus (Hassler)
Component of the parietal lobe. The first coronal slice between the superior temporal gyrus and the postcentral gyrus where the supramarginal gyrus appears was the rostral boundary whereas the slice where the supramarginal gyrus becomes continuous with the superior parietal gyrus was the caudal boundary. The medial and lateral boundaries were the lateral banks of the intraparietal sulcus and the medial banks of the lateral fissure and/or the superior temporal gyrus respectively (Christine Fennema-Notestine).
anterior part of inferior parietal lobule
one of the circumventricular organs of the brain. The OVLT is outside the blood brain barrier, and so neurons in this region can respond to factors that are present in the systemic circulation.
NIF has two classes here; Editor note: consider relationship to lamina terminalis
olfactory ventricle (olfactory part of lateral ventricle)
anterior ventral periventricular nucleus of hypothalamus
anteroventral periventricular nucleus of the hypothalamus
nucleus periventricularis anteroventralis
ventral periventricular hypothalamic nucleus
Unpaired midbrain region situated in the ventromedial portion of the reticular formation. The VTA is medial to the substantia nigra and ventral to the red nucleus, and extends caudally from the posterior hypothalamus in the diencephalon. The VTA contains dopamine neurons that project to various limbic and cortical areas and is a critical component of the brain's reward circuitry.
Region of the mesencephalon that arises from a small area of the neural plate, spanning the midline immediately adjacent, and being slightly posterior to the dorsal tegmentum area[XAO:0004226, http://www.ncbi.nlm.nih.gov/pubmed/2351962].
anterior hypothalamic commissure (Ganser)
anterior hypothalamic decussation of Ganser
commissura supraoptica dorsalis pars dorsalis
commissura supraoptica superior pars dorsalis
Only a small part of the Parietooccipital Fissure (or parieto-occipital sulcus) is seen on the lateral surface of the hemisphere, its chief part being on the medial surface. The lateral part of the parietooccipital fissure (Fig. 726) is situated about 5 cm. in front of the occipital pole of the hemisphere, and measures about 1.25 cm. in length. The medial part of the parietooccipital fissure (Fig. 727) runs downward and forward as a deep cleft on the medial surface of the hemisphere, and joins the calcarine fissure below and behind the posterior end of the corpus callosum. In most cases it contains a submerged gyrus. [WP,unvetted].
two classes in ncit (in general ncit distinguishes between fissue and sulcus, whereas FMA treats these as exact synonyms)
dorsal supraoptic commissure (of ganser)
dorsal supraoptic decussation (of Meynert)
dorsal supraoptic decussation (of ganser)
dorsal supraoptic decussation of Meynert
commissura supraoptica dorsalis pars ventralis (Meynert)
supraoptic commissures, dorsal (Meynert)
Small indentation on the inferior surface of the cerebral cortex at the border of the occiptal and parietal lobes. It is considered as a landmark because the occipital lobe is located just behind the line that connects that notch with the parietoccipital sulcus (adapted from Wikipedia).
anterior median nucleus of oculomotor nerve
anterior median nucleus of oculomotor nuclear complex
ventral medial nucleus of oculomotor nerve
nucleus nervi oculomotorii medianus anterior
Component of the frontal lobe, lateral aspect (Christine Fennema-Notestine).
Component of the frontal lobe. The appearance and disappearance of the central sulcus is the rostral and caudal boundaries of the precentral gyrus respectively. The medial boundary is specific frontal gyri (superior, middle and inferior) whereas the lateral boundary is the medial bank of the central sulcus (Christine Fennema-Notestine).
The metathalamus is a composite structure of the thalamus, consisting of the medial geniculate nucleus and the lateral geniculate nucleus. [WP,unvetted].
we follow FMA in making this a subtype of nucleus, but in fact it is a group containing two nuclei
Geniculate thalamic nuclear group (metathalamus)
The midline nuclear group (or midline thalamic nuclei) a region of the thalamus consisting of the following nuclei: paraventricular nucleus of thalamus (nucleus paraventricularis thalami) - not to be confused with paraventricular nucleus of hypothalamus paratenial nucleus (nucleus parataenialis) reuniens nucleus (nucleus reuniens) rhomboidal nucleus (nucleus commissuralis rhomboidalis) subfascicular nucleus (nucleus subfascicularis) [WP,unvetted].
The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract.
periventricular hypothalamic nucleus, posterior part
periventricular nucleus, posterior subdivision
posterior periventricular hypothalamic nucleus
posterior periventricular nucleus of hypothalamus
posterior periventricular nucleus of the hypothalamus
Part of thalamus comprising ill defined cellular groups in the caudal thalamus at the meso-diencephalic junction. It is not a homogeneous structure but consists of several distinct cellular groups, including the suprageniculate and limitans nuclei, the magnocellular division of the medial geniculate body, portions of the pulvinar nucleus and an area of mixed cell types intercalated between the ventroposterior nucleus and the nucleus lateral posterior (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 97)
The cingulate sulcus is a sulcus (brain fold) on the medial wall of the cerebral cortex. The frontal and parietal lobes are separated by the cingulate sulcus from the cingulate gyrus. [WP,unvetted].
nucleus interstitialis of posterior commissure
A marginal sulcus that is part of a insula [Automatically generated definition].
central lobe marginal branch of cingulate sulcus
central lobe marginal ramus of cingulate sulcus
cortex of island marginal branch of cingulate sulcus
cortex of island marginal ramus of cingulate sulcus
insula lobule marginal branch of cingulate sulcus
insula lobule marginal ramus of cingulate sulcus
insula marginal branch of cingulate sulcus
insula marginal ramus of cingulate sulcus
insular cortex marginal branch of cingulate sulcus
insular cortex marginal ramus of cingulate sulcus
insular lobe marginal branch of cingulate sulcus
insular lobe marginal ramus of cingulate sulcus
insular region marginal branch of cingulate sulcus
insular region marginal ramus of cingulate sulcus
island of reil marginal branch of cingulate sulcus
island of reil marginal ramus of cingulate sulcus
marginal branch of cingulate sulcus of central lobe
marginal branch of cingulate sulcus of cortex of island
marginal branch of cingulate sulcus of insula
marginal branch of cingulate sulcus of insula lobule
marginal branch of cingulate sulcus of insular cortex
marginal branch of cingulate sulcus of insular lobe
marginal branch of cingulate sulcus of insular region
marginal branch of cingulate sulcus of island of reil
marginal ramus of cingulate sulcus of central lobe
marginal ramus of cingulate sulcus of cortex of island
marginal ramus of cingulate sulcus of insula
marginal ramus of cingulate sulcus of insula lobule
marginal ramus of cingulate sulcus of insular cortex
marginal ramus of cingulate sulcus of insular lobe
marginal ramus of cingulate sulcus of insular region
marginal ramus of cingulate sulcus of island of reil
White matter tract arising in red nucleus and projecting to spinal cord ventral horn
Part of spinal trigeminal tract located in the medulla
tractus spinalis nervi trigemini (myelencephali)
The collateral fissure (or sulcus) is on the tentorial surface of the hemisphere and extends from near the occipital pole to within a short distance of the temporal pole. Behind, it lies below and lateral to the calcarine fissure, from which it is separated by the lingual gyrus; in front, it is situated between the hippocampal gyrus and the anterior part of the fusiform gyrus. [WP,unvetted].
cnit has two distinct classes; FMA and NIF treat these as exact synonyms.
The rostral interstitial nucleus of medial longitudinal fasciculus (riMLF) is a portion of the medial longitudinal fasciculus which controls vertical gaze. They project to the vestibular nuclei. [WP,unvetted].
rostral interstitial nucleus of the medial longitudinal fasciculus
rostral interstitial nucleus of medial longitudinal fasciculus
The solitary tract is a compact fiber bundle that extends longitudinally through the posterolateral region of the medulla. The solitary tract is surrounded by the nucleus of the solitary tract, and descends to the upper cervical segments of the spinal cord. [WP,unvetted].
The spino-olivary tract is located in the ventral funiculus of the spinal cord. This tract carries proprioception information from muscles and tendons as well as cutaneous impulses to the olivary nucleus. [WP,unvetted].
White matter bundle in the posterior hypothalamus containing ascending afferent fibers to the mammillary bodies from the ventral and dorsal tegmental nuclei (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 671).
A sulcus that divides the frontal lobe and parietal lobe above from the temporal lobe below. It is in both hemispheres of the brain but is longer in the left hemisphere. The lateral sulcus is one of the earliest-developing sulci of the human brain. It first appears around the fourteenth gestational week[WP,modified].
Nucleus in the midbrain at the level of the inferior colliculus near the midline, containing the motor neurons giving rise to the trochlear nerve, innervating the contralateral superior oblique extraocular muscle of the eye (Brodal, Neurological Anatomy, 3rd ed, 1981, pg. 533).
The anterior basal part of the insular cortex, which separates the lateral surface of the insula from the anterior perforated substance (Heimer, The Human Brain and Spinal Cord, 2nd ed., 1995, pg 80).
A spinal cord segment that adjacent_to a cervical region.
segmenta cervicalia medullae spinalis [1-8
Thin sheet of white matter dividing the external and internal segments of the globus pallidus in primates
internal medullary lamina of corpus striatum
internal medullary lamina of globus pallidus
internal medullary lamina of lentiform nucleus
lamina medullaris interna corporis striati
lamina medullaris medialis corporis striati
medial medullary lamina of corpus striatum
medial medullary lamina of globus pallidus
globus pallidus, lamina medullaris interna
internal medullary l. of corpus striatum
medial medullary lamina of the globus pallidus
medial medullary stria of corpus striatum
Component of the temporal lobe on the mesial surface. The rostral and caudal boundaries of the entorhinal cortex are the rostral end of the collateral sulcus and the caudal end of the amygdala respectively. The medial boundary is the medial aspect of the temporal lobe and the lateral boundary is the collateral sulcus. (DK).
TODO - check area vs complex. MBA:909 this is part of the hippocampal formation via retrohippocampal region
In primates it is found on the medial surface of the temporal lobe, partially bounded ventrolaterally by the collateral sulcus in the human and by the rhinal sulcus in the macaque. It is subdivided on the basis of internal structure into eight parts in the human ( Insausti-2004 ),and seven parts in the macaque ( Paxinos-2009a ). In the rat and mouse it is divided into a lateral part of the entorhinal area and a medial part of the entorhinal area; the latter is further divided into dorsal and ventral zones to produce three subdivisions in the rodent ( Swanson-2004 )
A regional part of brain that is part of a thalamus [Automatically generated definition].
Either of the two roots that come of the vestibulocochlear nerve
The intralaminar nucleus is a nucleus of the thalamus that contains the following nuclei: central lateral centromedian (or 'central medial') paracentral parafascicular. Some sources also include a 'central dorsal' nucleus. [WP,unvetted].
Intralaminar group of the dorsal thalamus
Intralaminar nuclei of the dorsal thalamus
The superior temporal sulcus is the sulcus separating the superior temporal gyrus from the middle temporal gyrus in the temporal lobe of the brain. The superior temporal sulcus is the first sulcus inferior to the lateral fissure. It is involved in the perception of where others are gazing and is thus important in determining where others' emotions are being directed. It is also involved in the perception of biological motion.
The lateral nuclear group is a collection of nuclei on the lateral side of the thalamus. According to MeSH, it consists of the following: lateral dorsal nucleus lateral posterior nucleus pulvinar [WP,unvetted].
lateral nuclear group of dorsal thalamus
Component of the cingulate cortex. The rostral and caudal boundaries were the posterior division of the cingulate cortex and the parahippocampal gyrus respectively. The medial and lateral boundaries were the medial wall (area unknown) and the precuneus respectively (Christine Fennema-Notestine).
The medial dorsal nucleus (or dorsomedial nucleus of thalamus) is a large nucleus in the thalamus. It receives inputs from the Pre-Frontal Cortex and the Limbic System and in turn relays them to the Pre-Frontal Association Cortex. As a result, it plays a crucial role in attention, planning, organization, abstract thinking, multi-tasking and active memory. The connections of the medial dorsal nucleus have even been used to delineate the prefrontal cortex of the Göttingen minipig brain. By stereology the number of brain cells in the region has been estimated to around 6.43 million neurons in the adult human brain and 36.3 million glial cells, and with the newborn having quite different numbers: around 11.2 million neurons and 10.6 million glial cells. Lesions of the medial dorsal nucleus have been associated with Wernicke's encephalopathy [WP,unvetted].
Editor node: consider generic medial nuclear group and adding medioventral as sibling of this
The posterior cingulate cortex is the backmost part of the cingulate cortex, lying behind the anterior cingulate cortex. This is the upper part of the 'limbic lobe'. The cingulate cortex is made up of an area around the midline of the brain. Surrounding areas include the retrosplenial cortex and the precuneus. Cytoarchitectonically posterior cingulate cortex is associated with Brodmann areas 23 and 31. [WP,unvetted].
A white fibre bundle descending in the precommissural septum toward the base of the forebrain, immediately rostral to the lamina terminalis; at the base, the bundle turns in the caudolateral direction; traveling through the ventral substantia innominata alongside the optic tract, it fades before reaching the amygdala.
One of two layers of both white and gray matter of the septum pellucidum. During fetal development there is a space between the two laminae called the cavum septum pellucidum which, in ninety per cent of cases, disappears during infancy.
A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert.
The mouth of the flasklike dentate nucleus of the cerebellum, directed inward (rostromedial), and giving exit to many of the fibers that compose the superior cerebellar peduncle or brachium conjunctivum.
intermediate periventricular nucleus of hypothalamus
periventricular nucleus at the tuberal level
Intermediate periventricular nucleus of the hypothalamus
intermediate periventricular hypothalamic nucleus
periventricular hypothalamic nucleus, intermediate part
neodentate portion of the dentate nucleus
Part of medial lemniscus located within the medulla
A regional part of brain that is part of a cerebellar cortex [Automatically generated definition].
A medial longitudinal fasciculus that is part of a medulla [Automatically generated definition].
medial longitudinal fasciculus of medulla oblongata
fasciculus longitudinalis medialis (myelencephali)
medial longitudinal fasciculus of the medulla
medial longitudinal fasciculus of medulla
Component of the temporal lobe, lateral aspect. The rostral boundary is the rostral extent of the inferior temporal sulcus whereas the caudal boundary is designated as the temporo-occipital incisure on the cortical surface. The occipitotemporal sulcus is the medial boundary and the inferior temporal sulcus is the lateral boundary (Christine Fennema-Notestine).
lateral occipitotemporal gyrus (heimer-83)
The olivocerebellar tract (olivocerebellar fibers) leaves the olivary nucleus and pass out through the hilum and decussate with those from the opposite olive in the raphé, then as internal arcuate fibers they pass partly through and partly around the opposite olive and enter the inferior peduncle to be distributed to the cerebellar hemisphere of the opposite side from which they arise. They terminate directly on Purkinje cells as the climbing fiber input system. [WP,unvetted].
It ascends the dorsal part of the lateral funiculus and enters the cerebellum via the restiform body. Within the cerebellum, its axons terminate in the ipsilateral hindlimb area of the anterior lobe and in the pyramis and the paramedian lobule predominantly ipsilaterally. Rostrally, it extends to lobules I and II. Afferents from the upper trunk, forelimbs, and the neck to the cerebellum.
The dorsal spinocerebellar tract (posterior spinocerebellar tract, Flechsig's fasciculus, Flechsig's tract) conveys proprioceptive information from the body to the cerebellum. It is part of the somatosensory system and runs in parallel with the ventral spinocerebellar tract. Proprioceptive information is taken to the via central processes of dorsal root ganglia (first order neurons). These central processes travel through the dorsal horn where they synapse with second order neurons of Clarke's nucleus. Axon fibers from Clarke's Nucleus convey this proprioceptive information in the spinal cord in the peripheral region of the posteriolateral funiculus ipsilaterally until it reaches the cerebellum, where unconscious proprioceptive information is processed. This tract involves two neurons and ends up on the same side of the body. [WP,unvetted][Wikipedia:Dorsal_spinocerebellar_tract].
dorsal spinocerebellar tract of the medulla
Part of medulla comprising a white matter structure containing nerve fibers of the pyramidal tract crossing from one side of the brain to the other (MM)
decussatio pyramidum medullae oblongatae
pyramidal decussation (pourfour du petit)
A regional part of brain that is part of a epithalamus [Automatically generated definition].
Dorsal division of the medial geniculate nucleus, as first defined by Morest (1964) in the cat, but also described in the rat. It fills all but the medial edge of the posterior tip in cat, and joins the lateral thalamic nucleus anteriorly (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1261345/?page=3)
dorsal nucleus of medial geniculate complex
nucleus corporis geniculati medialis, pars dorsalis
nucleus geniculatus medialis fibrosus (hassler)
nucleus geniculatus medialis pars dorsalis
dorsal nucleus of the medial geniculate body
nucleus dorsalis coporis geniculati medialis
dorsal nucleus of medial geniculate body
corpus geniculatus mediale, pars magnocelluaris
magnocelluar nucleus of medial geniculate complex
medial division of medial geniculate body
medial magnocellular nucleus of medial geniculate body
medial nucleus of medial geniculate body
nucleus corporis geniculati medialis, pars magnocelluaris
nucleus geniculatus medialis magnocelluaris (hassler)
nucleus geniculatus medialis, pars magnocelluaris
corpus geniculatus mediale, pars magnocellularis
magnocellular nucleus of medial geniculate complex
magnocellular nucleus of the medial geniculate body
nucleus corporis geniculati medialis, pars magnocellularis
nucleus geniculatus medialis magnocellularis (Hassler)
nucleus geniculatus medialis, pars magnocellularis
nucleus medialis magnocellularis corporis geniculati medialis
magnocellular nucleus of medial geniculate body
Part of pyramidal tract (corticospinal tract) containing uncrossed fibers and traveling in the ventral funiculus of the spinal cord.
anterior corticospinal tract of the medulla
The inferior frontal sulcus is a sulcus between the middle frontal gyrus and the inferior frontal gyrus. [WP,unvetted].
Predominantly white regional part of thalamus consisting of a Y shaped bundle of fibers that runs the anterior-posterior length of thalamus and divides the thalamus into roughly three regions (MM: 2006-10-26)
internal medullary lamina of the thalamus
Thin bundle of myelinated axons that divides the medial pallidal segment into outer and inner portions (Carpenter, Core Text of Neuroanatomy, 3rd ed., 1985, pg. 303).
accessory medullary lamina of corpus striatum
accessory medullary lamina of globus pallidus
incomplete medullary lamina of globus pallidus
lamina medullaris accessoria corporis striati
incomplete medullary lamina of the globus pallidus
The lateral medullary lamina is a thin white structure located in the basal ganglia of the primate brain. Bounded laterally by the putamen and medially by the globus pallidus, it is defined on the basis of Nissl or myelin stain ( Carpenter-1983 ).
external medulary lamina of globus pallidus
external medulary lamina of lentiform nucleus
external medullary lamina of corpus striatum
external medullary lamina of globus pallidus
external medullary lamina of lentiform nucleus
lamina medullaris externa corporis striati
lamina medullaris lateralis corporis striati
lateral medulary lamina of globus pallidus
lateral medullary lamina of corpus striatum
lateral medullary lamina of globus pallidus
globus pallidus, lamina medullaris externa
lateral medullary lamina of the globus pallidus
The fusiform gyrus is part of the temporal lobe. It is also known as the (discontinuous) occipitotemporal gyrus. Other sources have the fusiform gyrus above the occipitotemporal gyrus and underneath the parahippocampal gyrus. [WP,unvetted].
medial occipitotemporal gyrus-1 (heimer)
A long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the vestibular nucleus of the pons towards target cells in the spinal cord[GO].
Component of the temporal lobe, lateral aspect. The rostral boundary is the rostral extent of the ssuperior temporal sulcus. The caudal boundary is the cauday portion of the superior temporal gyrus (posterior to becoming continuous with the supramarginal gyrus). The medial boundary is the lateral fissure (and when present the supramarginal gyrus), and the lateral boundary is the superior temporal suclus (Christine Fennema-Notestine).
The part of the hypothalamus posterior to the middle region consisting of several nuclei including the medial mamillary nucleus, lateral mamillary nucleus, and posterior hypothalamic nucleus (posterior hypothalamic area). The posterior hypothalamic area is concerned with control of sympathetic responses and is sensitive to conditions of decreasing temperature and controls the mechanisms for the conservation and increased production of heat.
Component of the temporal lobe, lateral aspect. The rostral boundary is the rostral extent of the superior temporal sulcus whereas the caudal boundary is the temporo-occipital incisure on the cortical surface. The superior temporal sulcus is the medial boundary and the inferior temporal sulcus is the lateral boundary (Christine Fennema-Notestine).
The medial orbital gyrus presents a well-marked antero-posterior sulcus, the olfactory sulcus, for the olfactory tract. [WP,unvetted].
The transverse temporal gyri (also called Heschl's gyri or Heschl's convolutions) are found in the area of primary auditory cortex in the superior temporal gyrus of the human brain, occupying Brodmann areas 41 and 42. It is the first cortical structure to process incoming auditory information. Anatomically, the transverse temporal gyri are distinct in that they run mediolaterally (towards the center of the brain) rather than dorsiventrally (front to back) as all other temporal lobe gyri run. The Heschl's gyri are named after Richard L. Heschl.
anterior transverse convolution of heschl
anterior transverse temporal convolution of heschl
posterior transverse convolution of heschl
posterior transverse temporal convolution of heschl
A pathway that terminates on the hair cells of the cochlea or equivalent organ in the inner ear.
Nuclei in the ventral part of the thalamus, involved in modulating activity of dorsal thalamic nuclei.
The ventral nuclear group is a collection of nuclei on the ventral side of the thalamus. According to MeSH, it consists of the following: ventral anterior nucleus ventral lateral nucleus ventral posterior nucleus [WP,unvetted][Wikipedia:Ventral_nuclear_group].
consider splitting nucleus from nuclear group (FMA has 'nucleus of subthalamus') - but note this is also treated as a nucleus (singular) in FMA. ZFA:0005576 represents an individual nucleus within the group
Part of the globus pallidus, consisting of the more medial of the two segments. In some species, e.g., primates, it is separated from the lateral segment by the fibers of the medial medullary lamina (MM).
One of two recognized nuclei comprising the superior olive. The lateral superior olivary nucleus is much less prominent in humans than in many rodents and carnivores. In the latter species, it is frequently described as S- or V-shaped.
inferior olivary complex dorsalaccessory nucleus
A regional part of brain that is part of a forebrain [Automatically generated definition].
caudal part of ventral posterolateral nucleus
ventral posterior lateral nucleus (ilinsky)
ventral posterolateral nucleus, caudal part
ventral posterolateral thalamic nucleus, caudal part
caudal part of the ventral posterolateral nucleus
nucleus ventralis posterior lateralis, pars caudalis
nucleus ventralis posterior pars lateralis (Dewulf)
nucleus ventralis posterolateralis (Walker)
nucleus ventrocaudalis externus (Van Buren)
ventral posterolateral thalamic nucleus, posterior part
caudal part of ventral posterolateral nucleus of thalamus
One of two subnuclei of the superior olive located within the caudal pontine tegmentum. Appears as a parasagittal row of transversely oriented bipolar neurons in transverse sections of human, with elongated somata in humans and other primates and large caliber dendrites.
A regional part of brain that is part of a diencephalon [Automatically generated definition].
A multi-tissue structure that is part of a lateral hypothalamic area.
obsolete regional part of lateral hypothalamic region
Nerve fibers arising from motor neurons in the abducens nucleus that are contained within the pontine tegmentum
the crossing of the two trochlear nerves at their exit through the velum medullare anterius.
decussatio fibrarum nervorum trochlearium
Mostly gray regional part of anterior thalamic region, consisting of the anterior medial, anterior dorsal and anterior lateral thalamic nuclei in primates. In rodents, it consists of anterior medial and anterior ventral divisions, with several subdivisions of each, according to Paxinos (MM: 2006-10-26)
A regional part of brain that is part of a posterior hypothalamic region [Automatically generated definition].
segment of posterior hypothalamic region
obsolete regional part of posterior hypothalamic region
white matter structure containing fibers arising from the cochlear nuclear complex
A regional part of brain that is part of a telencephalon [Automatically generated definition].
segmenta lumbalia medullae spinalis [1-5]
Part of dorsal longitudinal fasciculus located within the pons
dorsal longitudinal fasciculus of the pons
fasciculus longitudinalis dorsalis (pontis)
A medial longitudinal fasciculus that is part of a pons [Automatically generated definition].
medial longitudinal fasciculus of pons of varolius
pons of varolius medial longitudinal fasciculus
fasciculus longitudinalis medialis (pontis)
medial longitudinal fasciculus of the pons
Component of the frontal lobe. The rostral and caudal boundaries of the frontal pole are the superior frontal gyrus and the rostral division of the middle frontal gyrus respectively (Christine Fennama-Notestine).
The dorsal trigeminal tract (dorsal trigeminothalamic tract, or lemniscus) is a tract which receives signals from Meissner's corpuscles and Pacinian corpuscles. this tract arises from Principal trigeminal nucleus and terminates in the VPM nucleus of the thalamus. [WP,unvetted].
uncrossed dorsal trigeminothalamic tract
This tract arises from Principal trigeminal nucleus and terminates in the ipsilateral VPM nucleus of the thalamus.[WP]
Part of spinothalamic tract that is in the pontine tegmentum
pons of varolius spinothalamic tract of medulla
spinothalamic tract of medulla of pons of varolius
tractus spinalis nervi trigemini (pontis)
Parietal lobe of the left hemisphere of the brain
Parietal lobe of the right hemisphere of the brain
A limbic lobe that is part of a left cerebral hemisphere.
A limbic lobe that is part of a right cerebral hemisphere.
An occipital lobe that is part of a left cerebral hemisphere.
An occipital lobe that is part of a right cerebral hemisphere.
A temporal lobe that is part of a left cerebral hemisphere.
A temporal lobe that is part of a right cerebral hemisphere.
A frontal cortex that is part of a right cerebral hemisphere.
A frontal cortex that is part of a left cerebral hemisphere.
A cerebral hemisphere that is in the left side of a brain.
A cerebral hemisphere that is in the right side of a brain.
posterior superior fissure of cerebellum
Fissure between cerebellar hemispheric lobules VIIA and VIIBi.
Fissure between cerebellar lobules VIIBii and VIII.
Fissure between cerebellar lobules VIII and IX.
Fissure between cerebellar lobules IX and X.
The cupula is a structure in the vestibular system, sensing proprioception. The cupula is located within the ampullae of each of the three semicircular canals. As fluid rushes by the cupula, hair cells within it sense rotational acceleration, and transmit the corresponding signal to the brain through the vestibulocochlear nerve (CN VIII) In their natural orientation within the head, the cupulae are located on the medial aspect of the semicircular canals. In this orientation, the kinocilia rest on the posterior aspect of the cupula. [WP,unvetted].
The inner part of the basilar membrane of the cochlea that supports the spiral organ of Corti.
basilar membrane of cochlea, zona arcuata
zona arcuata of basilar membrane of cochlea
The part of the macula lutea that excludes the fovea.
The ganglion of the vestibular nerve. It contains the cell bodies of the bipolar primary afferent neurons whose peripheral processes form synaptic contact with hair cells of the vestibular sensory end organs[WP,unvetted]. Distributed to the maculae of the utricle and saccule and to the ampullary crests of the semicircular ducts. The vestibular fibers arise in bipolar cells in the vestibular ganglion in the internal acoustic meatus.
vestibular part of vestibulocochlear ganglion
vestibulocochlear VIII ganglion vestibular component
nucleus nervi oculomotorii, pars medialis
vestibulocochlear ganglion vestibular component
The part of the vestibular ganglion that receives fibers from the maculae of the utricle and the sacculae and the ampullae of the anterior and lateral semicircular ducts.
the group of neuron cell bodies associated with the eighth cranial nerve during embryogenesis; splits in later development to form the cochlear and vestibular ganglia
The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO]
(During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG]
The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus
nucleus nervi oculomotorii ventrolateralis
nucleus nervi oculomotorii, pars ventralis
The ventral cochlear nucleus (or anterior, or accessory), placed between the two divisions of the cochlear nerve, is on the ventral aspect of the inferior peduncle. Composed of several regions of distinct cell types, this nucleus serves primarily as a relay station for ascending auditory information. Bushy cells in the anterior ventral cochlear nucleus (AVCN), which receive end bulbs of held from auditory nerve fibers, project to the superior olivary complex through the trapezoid body and intermediate acoustic stria. Other cell types project to the lateral lemniscus and the inferior colliculus directly. [WP,unvetted].
The dorsal cochlear nucleus (DCN, also known as the 'tuberculum acousticum'), is a cortex-like structure on the dorso-lateral surface of the brainstem. Along with the ventral cochlear nucleus, it forms the cochlear nucleus, where all auditory nerve fibers from the cochlea form their first synapses. [WP,unvetted].
anterior part of anterior cochlear nucleus
anterior part of the ventral cochlear nucleus
posterior part of anterior cochlear nucleus
posterior part of the ventral cochlear nucleus
ventral cochlear nucleus, posterior part
A small nucleus of the periolivary complex located laterally to the MNTB, and ventral to the MSO.
Nucleus in the pontine tegmentum of most mammals that receives projections from the ventral cochlear nucleus via the large specialized synapse, the Calyx of Held. It is not clear whether a well defined nucleus is present in humans, although humans may possess scattered cells with similar input.
A dorsal root ganglion that is part of a thorax [Automatically generated definition].
The group of nerve cell bodies located on the dorsal spinal roots within the vertebral column at the level of the lumbar vertebrae.
The group of nerve cell bodies located on the dorsal spinal roots within the vertebral column at the level of the fifth lumbar vertebra
The accessory cuneate nucleus is located lateral to the cuneate nucleus in the medulla oblongata at the level of the sensory decussation. It receives input from cervical spinal nerves and transmits that information to the cerebellum. These fibers are called cuneocerebellar (cuneate nucleus > cerebellum) fibers. In this function, the accessory cuneate nucleus is comparable to the upper extremity portion of the posterior spinocerebellar tract. [WP,unvetted].
external cuneate nucleus (Monakow, Blumenau 1891)
arcuate nucleus of hypothalamus of medulla
arcuate periventricular nucleus of medulla
infundibular hypothalamic nucleus of medulla
infundibular periventricular nucleus of medulla
medulla infundibular hypothalamic nucleus
medulla infundibular periventricular nucleus
arcuate hypothalamic nucleus medial part
Spinal nucleus of the trigeminal caudal part
caudal part of the spinal trigeminal nucleus
nucleus caudalis tractus spinalis nervi trigemini
nucleus spinalis nervi trigemini, pars caudalis
spinal nucleus of the trigeminal nerve caudal part
spinal nucleus of the trigeminal, caudal part
caudal part of spinal trigeminal nucleus
kvlliker-Fuse subnucleus of parabrachial nucleus
nucleus reticularis diffusus (Koelliker)
A cranial nerve nucleus for the vagus nerve in the medulla that lies under the floor of the fourth ventricle. It mostly serves parasympathetic vagal functions in the gastrointestinal tract, lungs, and other thoracic and abdominal vagal innervations. The cell bodies for the preganglionic parasympathetic vagal neurons that innervate the heart reside in the nucleus ambiguus.[WP,unvetted].
The FMA includes a separate sensoryt nucleus
dorsal motor nucleus of the vagus (vagal nucleus)
Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453)
In the brain, the inferior salivatory nucleus is a cluster of neurons controlling the parasympathetic input to the parotid gland. It is one of the components of the glossopharyngeal nerve. [WP,unvetted].
nucleus salivatorius inferior nervi glossopharyngei
Spinal nucleus of the trigeminal interpolar part
interpolar part of the spinal trigeminal nucleus
nucleus interpolaris tractus spinalis nervi trigemini
nucleus of spinal tract of N. V (subnucleus interpolaris)
nucleus spinalis nervi trigemini, pars interpolaris
spinal nucleus of the trigeminal nerve interpolar part
spinal nucleus of the trigeminal, interpolar part
spinal trigeminal nucleus, interpolar part
interpolar part of spinal trigeminal nucleus
In the substance of the formatio reticularis are two small nuclei of gray matter. The one near the dorsal aspect of the hilus of the inferior olivary nucleus is called the Sublingual nucleus (inferior central nucleus, nucleus of Roller.) [WP,unvetted].
nucleus parvocellularis nervi hypoglossi
The output region of the amygdala responsible for controlling responses (Phelps & LeDoux, 2005, http://www.ncbi.nlm.nih.gov/pubmed/ 16242399).
Discrete clusters of cells intercalated among the major amygdaloid nuclei. They stain darkly in Nissl stains and have been identified in all mammals. The main groups lie between the lateral-basolateral nuclear coplex and the central and medial nuclei. Additional cell groups have been described by some in other locations (Millhouse, O. E. The intercalated cells of the amygdala. J Comp Neurol 247: 246-271, 1986)., Groups of cells located between the lateral basolateral amygaloid nuclear complex and the central nucleus of the amygdala. They stain darkly in Nissl stains and have been identified in all mammals. (Millhouse, O. E. The intercalated cells of the amygdala. J Comp Neurol 247: 246-271, 1986)
intercalated masses of nucleus amygdaloideus
nucleus amygdaloideus basalis, pars medialis
The sensory interface of the amygdala where plasticity is mediated (Phelps & LeDoux, 2005, http://www.ncbi.nlm.nih.gov/pubmed/ 16242399).
lateral part of basal amygdaloid nucleus
basomedial amygdaloid nucleus anterior part
basomedial amygdaloid nucleus anterior subdivision
basomedial amygdaloid nucleus, anterior part
medial part of the basal amygdalar nucleus
nucleus amygdalae basalis, pars medialis
nucleus amygdaloideus basalis pars lateralis parvocellularis
Three layered structure that is located in the caudal aspect of the amygdala bordering the periamygdaloid cortex laterally.
posterior cortical nucleus of the amygdala
medial amygdaloid nucleus principal part
nucleus of the lateral olfactory tract (ganser)
nucleus of tractus olfactorius lateralis
part of amygdala in FMA but this leads to inconsistency when combined with ABA partitions
Aggregate brain region defined as those areas of cerebral cortex receiving direct synaptic input from the olfactory bulb (Price, 1973). It usually includes the piriform cortex and sometimes other areas.
consider relationship: receives_input_from UBERON:0002264 olfactory bulb
That portion of the cerebral cortex that, with the palaeocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archaeocortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals[BTO:0001446].
The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors[GO][GO:0021989].
(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]
Brodmann's area 28; major gateway for neocortical input to the hippocampus; origin of the perforant pathway; a component of the medial temporal lobe memory system. (CSP) * The cytoarchitecturally well-defined area of multilaminate cerebral cortex on the medial aspect of the parahippocampal gyrus, immediately caudal to the olfactory cortex of the uncus. The entorhinal cortex is the origin of the major neural fiber system afferent to the hippocampus, the so-called PERFORANT PATHWAY. (Stedman, 25th ed).
FMA considers this a syn of entorhinal cortex. See also brodman definition
secondary olfactory cortical area (carpenter)
the region of the subarachnoid space that is located below and anterior to the optic chiasm
The hippocampal sulcus, also known as the hippocampal fissure, is a sulcus that separates the dentate gyrus from the subiculum and the CA1 field in the hippocampus. [WP,unvetted].
two classes in ncit (in general ncit distinguishes between fissure and sulcus, whereas FMA treats these as exact synonyms)
The anterior end of the hemisphere is named the frontal pole. The posterior end is named the occipital pole. The anterior end of the temporal lobe, the temporal pole. [WP,unvetted].
In the occipital lobe, the lateral occipital sulcus extends from behind forward, and divides the lateral surface of the occipital lobe into a superior and an inferior gyrus, which are continuous in front with the parietal and temporal lobes. [WP,unvetted].
ascending limb of the inferior temporal sulcus
The term terminal ascending limb of the lateral fissure refers to one of two branches of the lateral fissure at its posterior terminus identified by dissection in the human. The other is the terminal descending limb of the lateral fissure ( Ono-1990 ). It is not found in the macaque ( Martin-2000 ), the rat ( Swanson-2004 ) or the mouse ( Hof-2000 ).
ascending terminal ramus of sylvian fissure
posterior ascending limb of lateral fissure
posterior ramus of lateral cerebral sulcus
ramus posterior ascendens fissurae lateralis
terminal ascending limb of sylvian fissure
terminal ascending limb of the lateral fissure
posterior ascending limb of lateral sulcus
The parietal operculum, forming the superior bank of the sylvian fissure, as studied in the cat, contains the secondary somatosensory representation, 'S-II', and a second somatotopic representation (parietal ventral, or PV). Anatomically, primate S-II receives inputs from area 3 and area 1, and projects to PV and area 7. PV has projections to area 5 and premotor areas. [WP,unvetted].
The marginal sulcus is the portion of the cingulate sulcus adjacent to the paracentral lobule and the precuneus. It is sometimes known as the 'marginal part of the cingulate sulcus'. [WP,unvetted].
The intraparietal sulcus (IPS) is located on the lateral surface of the parietal lobe, and consists of an oblique and a horizontal portion. The IPS contains a series of functionally distinct subregions that have been intensively investigated using both single cell neurophysiology in primates and human functional neuroimaging. Its principal functions are related to perceptual-motor coordination (for directing eye movements and reaching) and visual attention. The IPS is also thought to play a role in other functions, including processing symbolic numerical information, visuospatial working memory and interpreting the intent of others. [WP,unvetted].
The postcentral sulcus of the parietal lobe lies parallel to, and behind, the central sulcus in the human brain. (A sulcus is one of the prominent grooves on the surface of the brain. ) The postcentral sulcus divides the postcentral gyrus from the remainder of the parietal lobe. [WP,unvetted].
postcentral fissure of cerebral hemisphere
The central sulcus is a fold in the cerebral cortex of brains in vertebrates. Also called the central fissure, it was originally called the fissure of Rolando or the Rolandic fissure, after Luigi Rolando. The central sulcus is a prominent landmark of the brain, separating the parietal lobe from the frontal lobe and the primary motor cortex from the primary somatosensory cortex. [WP,unvetted].
A regional part of brain that is part of a inferior colliculus [Automatically generated definition].
obsolete regional part of inferior colliculus
The Medial parabrachial nucleus is a nucleus of the pons which constitutes part of the pneumotaxic center. It gets its name from its location relative to the superior cerebellar peduncles, which is also known as the 'brachia conjunctiva'. [WP,unvetted].
The callosal sulcus is a sulcus in the brain between the cingulate gyrus and corpus callosum, below the longitudinal cerebral fissure. [WP,unvetted].
The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted].
A small triangular area in front of the anterior perforated substance. Its apex, directed forward, occupies the posterior part of the olfactory sulcus, and is brought into view by throwing back the olfactory tract (adapted from Wikipedia)
The terminal nerve, located anterior to cranial nerve I, is comprised of a group of cells with somata adjacent to the olfactory bulb and processes that extend anteriorly to the olfactory epithelium and posteriorly to the telencephalon. In teleost fish an additional group of axons extends along the optic tract and delivers putative neuromodulators to the retina. It is thought to develop from cranial neural crest.
The terminal nerve, located anterior to cranial nerve I, is comprised of a group of cells with somata adjacent to the olfactory bulb and processes that extend anteriorly to the olfactory epithelium and posteriorly to the telencephalon. In teleost fish an additional group of axons extends along the optic tract and delivers putative neuromodulators to the retina. It is thought to develop from cranial neural crest. Whitlock 2004. Also see Grens, Greenwood and Fernald, Brain Behav Evol 2005; 66(1):1-9.[TAO]
http://www.ncbi.nlm.nih.gov/pubmed/2286018 state: 'The presence of an additional cranial nerve (the nervus terminalis or cranial nerve zero) is well documented in many non-human vertebrate species. However, its existence in the adult human has been disputed. The present study focused on the structure and incidence of this nerve in the adult human brain. The nerve was examined post-mortem in 10 adult brains using dissection microscopy, light microscopy, transmission electron microscopy, and immunohistochemistry. In all specimens, the nervus terminalis was identified bilaterally as a microscopic plexus of unmyelinated peripheral nerve fascicles in the subarachnoid space covering the gyrus rectus of the orbital surface of the frontal lobes. The plexus appeared in the region of the cribriform plate of the ethmoid and coursed posteriorly to the vicinity of the olfactory trigone, medial olfactory gyrus, and lamina terminalis. We conclude that the terminal nerve is a common finding in the adult human brain, confirming early light microscopic reports.'
A nucleus of brain that is part of a trigeminal nuclear complex.
massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA.
nucleus tractus mesencephali nervi trigeminalis
A sensory epithelium that is part of a gustatory system.
Bundles of axons traversing the pontine tegmentum oriented in the mediolateral direction. These fibers are related to the auditory pathway. Nuclei are embedded within these fibers.
nucleus interstitialis commissurae anterior
ventral nucleus of oculomotor nuclear complex
magnocellular division of ventral anterior nucleus of thalamus
nucleus lateropolaris magnocellularis (hassler)
nucleus rostralis lateralis situs perifascicularis
nucleus thalamicus ventral anterior, pars magnocellularis
nucleus ventralis anterior, pars magnocellularis
pars magnocellularis nuclei ventralis anterior thalami
ventral anterior nucleus, magnocellular part
ventral anterior nucleus, pars magnocellularis
ventral anterior thalamic nucleus, magnocellular part
ventroanterior thalamic nucleus, magnocellular part
magnocellular part of the ventral anterior nucleus
nucleus thalamicus ventralis anterior, pars magnocellularis
magnocellular part of ventral anterior nucleus
The magnocellular red nucleus (RNm) is located in the rostral midbrain and is involved in motor coordination. Together with the parvocellular red nucleus, it makes up the red nucleus.
nucleus ventralis anterior, pars parvicellularis
ventral anterior nucleus, pars parvicellularis
ventral anterior thalamic nucleus, parvicellular part
nucleus ventralis anterior, pars parvocellularis
parvicellular part of the ventral anterior nucleus
parvicellular part of ventral anterior nucleus
The parvocellular red nucleus (RNp) is located in the rostral midbrain and is involved in motor coordination. Together with the magnocellular red nucleus, it makes up the red nucleus.
nucleus ventralis posterior inferior thalami
ventral posterior inferior nucleus of thalamus
ventral posterior inferior thalamic nucleus
ventral posterior inferior nucleus of dorsal thalamus
ventral posterolateral thalamic nucleus, inferior part
The ventral posterolateral nucleus (VPL) is a nucleus of the thalamus. Together with the ventral posteromedial nucleus (VPM) it constitutes the ventral posterior nucleus. [WP,unvetted].
nucleus ventralis posterior lateralis thalami
nucleus ventralis posterolateralis thalami
nucleus ventralis thalami posterior lateralis
posterolateral ventral nucleus of thalamus
posterolateral ventral nucleus of the thalamus
ventral posterolateral nucleus of thalamus
ventral posterolateral nucleus of the thalamus
ventral posterior lateral nucleus of dorsal thalamus
ventral posterolateral nucleus of the thalamus principal part
ventral posterolateral nucleus of the thalamus, general
ventral posterolateral nucleus of the thalamus, principal part
ventroposterior lateral thalamic nucleus
ventroposterolateral nucleus of the thalamus
Component of the occipital lobe. The rostral boundary of the lingual gyrus was the posterior extent of the parahippocampal gyrus whereas the caudal boundary was the most posterior coronal slice where the gyrus could be visualized. The medial and lateral boundaries were the medial portion of the temporal and occipital cortices and the medial bank of the collateral sulcus respectively (Christine Fennema-Notestine).
Part of spinothalamic tract that is in the medulla
The ventral posteromedial nucleus is a nucleus of the thalamus. [WP,unvetted].
nucleus ventralis posterior medialis thalami
nucleus ventralis posteromedialis thalami
nucleus ventrocaudalis anterior internus (hassler)
posteromedial ventral nucleus of thalamus
posteromedial ventral nucleus of the thalamus
ventral posterior medial nucleus of thalamus
ventral posteromedial nucleus of thalamus
ventral posteromedial nucleus of the thalamus
ventroposteromedial nucleus of the thalamus
ventral posterior medial nucleus of dorsal thalamus
ventral posteromedial nucleus of the thalamus principal part
ventral posteromedial nucleus of the thalamus, general
ventral posteromedial nucleus of the thalamus, principal part
A regional part of brain that is part of a cerebellum [Automatically generated definition].
Portion of frontal lobe that overlaps the insular cortex (adapted from Wikipedia)
nucleus ventralis oralis, pars medialis (Dewulf)
A long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the superior colliculus of the midbrain towards target cells in the ventral spinal cord[GO].
NIF and FMA differ in placement (spinal cord vs medulla)
A regional part of brain that is part of a midbrain [Automatically generated definition].
A regional part of brain that is part of a intermediate hypothalamic region [Automatically generated definition].
intermediate hypothalamic region segment
segment of intermediate hypothalamic region
obsolete regional part of intermediate hypothalamic region
White matter structure containing axons arising from cochlear nuclear complex (Brodal, Neurological Anatomy, 3rd ed, 1985, pg 609)
A fiber bundle that runs through the medulla, pons and midbrain that arises in the cochlear nucleus and projects to various brainstem nuclei and ultimately the contralateral inferior colliculus of the midbrain. The brainstem nuclei include the superior olive, the medial nucleus of the trapezoid body, and the dorsal nucleus of the lateral lemniscus. Fibers leaving these brainstem nuclei ascending to the inferior colliculus rejoin the lateral lemniscus. In that sense, this is not a 'lemniscus' in the true sense of the word (second order, decussated sensory axons), as there is third (and out of the lateral superior olive, fourth) order information coming out of some of these brainstem nuclei. Adapted from Wikipedia.org (MM).
A relatively small region of the hypothalamus located inferior to the hypothalamic sulcus.
Brain structure which is the dorsal most region of the hypothalamus and expands laterally and emerges caudal to the ventral zone and is separated from the median tuberal portion by a deep ventral sulcus. From Neuroanatomy of the Zebrafish Brain[ZFA:0000347, ISBN:3764351209, ZFA:curator].
In humans it contains the following nuclei: portions of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), endopeduncular nucleus [TA]) (nucleus endopeduncularis [TA]), and portions of the nucleus of the ansa lenticularis (nucleus ansae lenticularis
The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer.
caudal central nucleus of oculomotor nerve
Part of medial lemniscus located within the pons
A portion of the cerebral cortex that, with the paleocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archicortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals. Being part of the limbic system, it has functions related to emotions and formation of memory. Signals being sent from the limbic lobe to the hippocampal formations can go via the archicortex as an intermediate.
A muscle in the manus that functions to adduct the thumb. It has two heads: transverse and oblique. It is a fleshy, flat, triangular, and fan-shaped muscle deep in the thenar compartment beneath the long flexor tendons and the lumbrical muscles at the center of the palm. It overlies the metacarpal bones and the interosseous muscles[WP].
dorsal nucleus of oculomotor nuclear complex
nucleus nervi oculomotorii, pars dorsalis
A regional part of brain that is part of a midbrain tectum [Automatically generated definition].
obsolete regional part of midbrain tectum
One of the convolutions on the medial surface of the cerebral hemisphere. It surrounds the rostral part of the brain and interhemispheric commissure and forms part of the limbic system. (MSH) One of three essential structures comprising the limbic lobe, the other two being the hippocampus and parahippocampal gyrus. (CSP)
The inferior surface of the temporal lobe is concave, and is continuous posteriorly with the tentorial surface of the occipital lobe. It is traversed by the inferior temporal sulcus, which extends from near the occipital pole behind, to within a short distance of the temporal pole in front, but is frequently subdivided by bridging gyri.
intermediate nucleus of oculomotor nuclear complex
nucleus nervi oculomotorii, pars intermedius
A nucleus of the superior olivary complex that surrounds the primary superior olivary nuclei
superior olivary complex periolivary region
In the anatomy of the brain, the centromedian nucleus, also known as the centrum medianum, (CM or Cm-Pf) is a part of the intralaminar nucleus (ILN) of the thalamus. There are two centromedian nuclei arranged bilaterally. It contains about 2000 neurons per cubic millimetre and has a volume of about 310 cubic millimetres with 664,000 neurons in total. [WP,unvetted].
central magnocellular nucleus of thalamus
Component of the temporal lobe on the mesial surface, posterior to the entorhinal cortex. The rostral and caudal boundaries are the posterior end of the netorhinal cortex and the caudal portion of the hippocampus, respectively. The medial boudnary is designated as the medial aspect off the temporal lobe and the lateral boundary is the collateral sulcus (Christine Fennema-Notestine).
The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells
Compare with ZFA:0000636 - cerebellar crest, which is also composed of parallel fibers but located in a more restricted nucleus within the cerebellum
medial nucleus of oculomotor nuclear complex
nucleus lateralis oralis situs principalis
nucleus ventralis lateralis, pars oralis
nucleus ventrooralis externus, anterior part (van buren)
ventral anterior nucleus, pars densicellularis
ventral lateral thalamic nucleus, oral part
oral part of the ventral lateral nucleus
The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells.
Purkinje cell layer of cerebellar cortex
Component of the inferior frontal gyrus.defined as the first gyrus from the precentral gyrus.
inferior frontal gyrus, pars opercularis
opercular portion of inferior frontal gyrus
pars opercularis gyri frontalis inferioris
posterior part of inferior frontal gyrus
opercular part of inferior frontal gyrus
One of a set of nuclei located in the posterior thalamus, that projects to all or nearly all extra-striate visual areas.
One of four subdivisions recognized in the primate pulvinar based on initially on topography, located ventrally between the medial and lateral geniculate bodies (Carpenter, A core text of neuroanatomy, 3rd ed., 1985, pg 238)
nucleus pulvinaris thalami, pars inferior
lateral posterior nucleus of the thalamus
laterodorsal nucleus nucleus of thalamus
nucleus dorsalis superficialis (hassler)
lateral group of nuclei, dorsal division
Ventral division of medial geniculate body, first described by Morest (1964) in the cat, but found in primate, mouse and rat as well. It begins midway in the posterior third of the medial geniculate in the cat and is prominant anteriorly. The boundary between the dorsal and ventral divisions is demarcated in rat by a thick horizontally oriented axon bundle, the midgeniculate bundle (Webster, 1995, fig 16).
medial nucleus of medial geniculate complex
nucleus corporis geniculati medialis, pars ventralis
nucleus geniculatus medialis fasciculosus (hassler)
nucleus geniculatus medialis pars ventralis
nucleus ventralis corporis geniculati medialis
ventral nucleus of medial geniculate complex
ventral principal nucleus of medial geniculate body
ventral nucleus of the medial geniculate body
ventral nucleus of medial geniculate body
Runs through the ventrolateral surface of the spinal cord. It enters the cerebellum through the superior cerebellar peduncle. It crosses the midline at the segmental level and recrosses in the cerebellum. Its terminals are distributed in the cerebellar anterior lobe, preferentially in the ipsilateral intermediate cortex. Rostrally, it extends to lobule II.
The ventral spinocerebellar tract conveys proprioceptive information from the body to the cerebellum. It is part of the somatosensory system and runs in parallel with the dorsal spinocerebellar tract. Both these tracts involve two neurons and end up on the same side of the body. The ventral tract (under L2/L3) gets its proprioceptive/fine touch/vibration information from a first order neuron, with its cell body in a dorsal ganglion. The axon runs via the fila radicularia to the dorsal horn of the grey matter. There it makes a synapse with the dendrites of two neurons: they send their axons bilaterally to the ventral border of the lateral funiculi. The ventral spinocerebellar tract then enters the cerebellum via the superior cerebellar peduncle. This is in contrast with the dorsal spinocerebellar tract (C8 - L2/L3), which only has 1 unilateral axon that has its cell body in the Clarke's nuclei (only at the level of C8 - L2/L3). The fibers of the ventral spinocerebellar tract then eventually enter the cerebellum via the superior cerebellar peduncle. This is one of the few afferent tracts through the superior cerebellar peduncle. Originates from ventral horn at lumbosacral spinal levels. Axons first cross midline in the spinal cord and run in the ventral border of the lateral funiculi. These axons ascend up to the pons where they join the superior cerebellar peduncle to enter the cerebellum. Once in the deep white matter of the cerebellum, the axons recross the midline, give off collaterals to the globose and emboliform nuclei, and terminate in the cortex of the anterior lobe and vermis of the posterior lobe. [WP,unvetted][Wikipedia:Ventral_spinocerebellar_tract].
A small muscle on the posterior aspect of the elbow joint.
Some consider anconeus to be a continuation of the triceps brachii muscle. Some sources consider it to be part of the posterior compartment of the arm, while others consider it part of the posterior compartment of the forearm.
Part of mammillothalamic tract contained within the hypothalamus
fasciculus mamillothalamicus (hypothalami)
mammillothalamic tract of the hypothalamus
One of the median nuclei of the thalamus, situated ventral and medial to the stria medullaris.
TODO - compare with UBERON:0002881 ! sublingual nucleus; also to dorsal raphe nucleus. Check if the same as ZFA 'inferior raphe nucleus'. See comments on https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3248146&group_id=36855
disjointness violation - relationship: part_of UBERON:0001966
Predominantly gray matter structure consisting of large multipoloar cells lying aong axons of the brachium of the superior colliculus, lyaing adjaent to the dorsal terminal nucleus of the accessory optic system. In several species, cells of this nucleus receive inpu from the contralateral retina (Sefton and Dreher in Paxinos, G. The rat nervous system, 1995, pg. 862).
Component of the frontal lobe, lateral aspect. The rostral boundary is the first appearance of the inferior frontal sulcus whereas the caudal boundary is the precentral gyrus. The medial and lateral boundaries are the lateral bank of the inferior frontal sulcus and the medial bank of the lateral orbital sulcus and/or the circular insular sulcus respectively (Christein Fennema-Notestine).
ncit has two classes, but these are exact synonyms in FMA
The oral pontine reticular nucleus is delineated from its caudal brother, with which it shares its first three names. This nucleus tapers into the lower mesencephalic reticular formation and contains sporadic giant cells. Different populations of the pontis oralis have displayed discharge patterns which coordinate with phasic movements to and from paradoxical sleep. From this information it has been implied that the n.r. pontis oralis is involved in the mediation of changing to and from REM sleep. [WP,unvetted].
A bundle or band of sensory nerve fibers. ribbon, from Greek lemniskos.
Fiber tract arising predominantly from neurons in the nucleus gracilis and nucleus cuneatus in the medulla, projecting to thalamus. Fibers cross in the decussation of the medial lemniscus.
The median raphe nucleus (or superior central nucleus) is composed of polygonal, fusiform and pyriform neurons and exists rostral to the nucleus raphe pontis. One trait of the MRN is its inhibition by lysergic acid diethylamide and psilocin, two serotonin antagonist hallucinogens. The inactivation of the nucleus centralis superior via LSD produces a dose dependent inactivation in the MRN, but not in the raphe pallidus[WP,unvetted].
TODO - The term medial raphe nucleus refers to a composite structure that consists of the superior central nucleus and the inferior central nucleus of the pontine reticular formation ( Carpenter-1983 )
Part of dorsal longitudinal fasciculus located in the midbrain tegmentum
midbrain posterior longitudinal fasciculus
posterior longitudinal fasciculus of midbrain
dorsal longitudinal fasciculus of the midbrain
fasciculus longitudinalis dorsalis (mesencephali)
dorsal longitudinal fasciculus of midbrain
nucleus of the lateral lemniscus, dorsal part
nucleus lemnisci lateralis pars dorsalis
nucleus of the lateral lemniscus dorsal part
The lateral parabrachial nucleus induces thirst by stimulating the median preoptic nucleus. It gets its name from its location relative to the superior cerebellar peduncles, which is also known as the 'brachia conjunctiva'. [WP,unvetted].
Part of dorsal longitudinal fasciculus located within the hypothalamus
dorsal longitudinal fasciculus of the hypothalamus
fasciculus longitudinalis dorsalis (hypothalami)
dorsal longitudinal fasciculus of hypothalamus
decussatio tegmentalis dorsalis (Meynert)
Nucleus located in the pontine tegmentum containing motor neurons that innervate the muscles of the face. Some neurons that project to the cerebellum have also been identified in some species.
see comments for facial nucleus. also check ZFA/pons
The flocculonodular lobe is a lobe of the cerebellum consisting of the nodule and the flocculus. It is closely associated with the vestibulocerebellum. [WP,unvetted].
receives input from the inferior and medial vestibular nuclei and sends fibers back to the vestibular nuclei, and processes and integrates these signals to allow for the constant maintenance of balance [MP:0009961]
The lobulus centralis is a small square lobule, situated in the anterior cerebellar notch. It overlaps the lingula, from which it is separated by the precentral fissure; laterally, it extends along the upper and anterior part of each hemisphere, where it forms a wing-like prolongation, the alar central lobule. [WP,unvetted].
anterior crescentic lobule of cerebellum
anterior quadrangular lobule of cerebellum
anterior quadrangular lobule of cerebellum [H IV et V]
lobulus quadrangularis anterior cerebelli [h iv et v]
A predominantly gray matter structure of the basal telencephalon defined on the basis of Nissl stain. Caudal to the anterior commissure it lies deep to the globus pallidus and dorsal to the amygdala. Rostral to the anterior commissure it lies deep to the striatum. The more rostral portion contains the basal forebrain nucleus ( Anthoney-1994 ). In the late twentieth century the region containing the substantia innominata was resegmented on the basis of neurochemistry and connectivity to constitute the striatopallidal system ( Heimer-1995 ). In this scheme the caudal portion of substantia innominata is located largely in the ventral pallidum and the rostral portion in the ventral striatum. (from Brain Info)
nucleus ventralis posterior medialis thalami, pars parvicellularis
pars parvicellularis nuclei ventralis posteromedialis thalami
parvicellular part of ventral posteromedial nucleus of thalamus
ventral posteromedial nucleus of thalamus, parvicellular part
ventral posteromedial nucleus, parvocellular part
ventral posteromedial thalamic nucleus, parvicellular part
ventroposteromedial nucleus of the thalamus, parvicellular part
nucleus ventralis posterior medialis, pars parvocellularis
parvicellular part of the ventral posteromedial nucleus
ventral posteromedial nucleus of the thalamus parvicellular part
ventral posteromedial nucleus of the thalamus, parvicellular part
ventroposterior medial thalamic nucleus, parvocellular part
ventroposteromedial nucleus of the thalamus parvicellular part
parvicellular part of ventral posteromedial nucleus
nucleus ventralis posterior lateralis, pars oralis
ventral part of ventral lateral posterior nucleus (jones)
ventral posterolateral nucleus, oral part
ventral posterolateral thalamic nucleus, oral part
oral part of the ventral posterolateral nucleus
oral part of ventral posterolateral nucleus
The subcallosal area (parolfactory area of Broca, area parolfactoria) is a small triangular field on the medial surface of the hemisphere in front of the subcallosal gyrus, from which it is separated by the posterior parolfactory sulcus; it is continuous below with the olfactory trigone, and above and in front with the cingulate gyrus; it is limited anteriorly by the anterior parolfactory sulcus. [WP,unvetted].
The central lobule is a small square lobule, situated in the anterior cerebellar notch. It overlaps the lingula, from which it is separated by the precentral fissure; laterally, it extends along the upper and anterior part of each hemisphere, where it forms a wing-like prolongation, the ala lobuli centralis. [WP,unvetted].
Note in FMA this is classified as a hemispheric lobule, which leads to inconsistencies. In ABA it is vermic, and FMA actually places it in the anterior vermis.
central lobule of cerebellum [II and III]
Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).
involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]
nucleus ventralis posteromedialis, pars prinicipalis
nucleus ventralis posteromedialis, pars principalis
principal part of the ventral posteromedial nucleus
ventral posteromedial nucleus, principal part
principal part of ventral posteromedial nucleus
The Brachium of inferior colliculus (or inferior brachium) carries auditory afferent fibers from the inferior colliculus of the mesencephalon to the medial geniculate nucleus. [WP,unvetted].
nucleus of the brachium of the inferior colliculus
The cingulate cortex is a part of the brain situated in the medial aspect of the cortex. It is extended from the corpus callosum below to the cingulate sulcus above, at least anteriorly. [WP,unvetted].
A commissure that is part of a inferior colliculus [Automatically generated definition].
commissure of posterior corpus quadrigeminum
posterior corpus quadrigeminum commissure
White matter structure in the brain consisting of fibers running along the lateral margin of the ventricular surface of the thalamus. The stria terminalis covers the thalamostriate vein, marking a line of separation between the thalamus and the caudate nucleus as seen upon gross dissection of the ventricles of the brain, viewed from the superior aspect. The stria terminalis extends from the region of the interventricular foramen to the temporal horn of the lateral ventricle, carrying fibers from the amygdala to the septal, hypothalamic, and thalamic areas of the brain. It also carries fibers projecting from these areas back to the amygdala. (http://en.wikipedia.org/wiki/Stria_terminalis)
Thalamic nucleus separated from the ventromedial part of the mediodorsal nucleus of the thalamus by the internal medullary lamina (Paxinos The rat nervous system 2nd ed, Academic Press, 1995).
nucleus centralis superior lateralis thalami
regional part of cerebellar white matter
A wall, dividing a cavity or structure into smaller ones[WP].
The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted].
segmenta thoracica medullae spinalis [1-12]
The horseshoe-shaped tract that connects the two olfactory bulbs.
Periaqueductal gray (PAG; also called the 'central gray') is the gray matter located around the cerebral aqueduct within the midbrain. It plays a role in the descending modulation of pain and in defensive behaviour. The ascending pain and temperature fibers of the spinothalamic tract also send information to the PAG via the spinomesencephalic tract. The spinomesencephalic tract is so-named because the fibers originate in the spine and terminate in the mesencephalon, another name for the midbrain, the part of the brain in which the PAG resides. [WP,unvetted].
substantia grisea centralis mesencephali
A nerve fiber that is part of a trigeminal nerve.
The major forebrain commissure that connects the two temporal lobes of the cortex.
Pathway arising from the fastigial nucleus to the vestibular nuclei, reticular formation, motor neurons of brainstem and cervical spinal cord (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 261).
A fiber bundle containing fibers from nuclei of the hypothalamus that project to the dorsal tegmental nucleus and other regions of the midbrain and the pons, as well as fibers originating in the pontine reticular formation and the medullary reticular formation that project to the thalamus and other regions of the forebrain (Carpenter-83). In NeuroNames it is a composite structure consisting of the dorsal longitudinal fasciculus of hypothalamus, the dorsal longitudinal fasciculus of midbrain, the dorsal longitudinal fasciculus of pons and the dorsal longitudinal fasciculus of medulla. (NeuroNames)
White matter structure containing fibers arising from neurons in the cochlear nuclear complex
A regional part of brain that is part of a pretectal region [Automatically generated definition].
obsolete regional part of pretectal region
A regional part of brain that is part of a hypothalamus [Automatically generated definition].
A rigid external coating which is secreted by the hypodermis, seam and some transitional epithelial cells which covers the outer body, the major openings into the body cavity from the exterior, and two large sensory bristles, the male spicules. The cuticle of the spicules, the hook, and of some portions of the spicule channels is especially rigid and is probably sclerotized. Similar sclerotic features are occasionally noted in the ventral surface of the male tail fan[WBbt]. The main structural components of the nematode cuticle are proteins, highly cross-linked collagens and specialised insoluble proteins known as cuticlins, together with glycoproteins and lipids[WP].
GO has a superclass protein-based cuticle development
A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]
Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic
The saccular invagination of ectoderm from which the vertebrate inner ear develops[BTO]. Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells[ZFA]. epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]
Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG]
The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG]
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
Proliferative region that is part of the ventricular system.
Proliferative zone in the region of the neural tube adjacent to the lumen.
There are two primary regions that are thought to give rise to neurons that make up the cerebellum. The first region is the ventricular zone (the roof of the fourth ventricle). This area produces Purkinje cells and deep cerebellar nuclear neurons[BTO:0003654].
in BTO this is restricted to the 4th ventricle - however this class also represents the early ventricular zone as well as its post-natal remnants. The MA class is named 'ventricular zone of brain' and is presumably restricted to the post-natal zone; DHBA class is forebrain; PBA class is neocortex; TAO/ZFA is neocortex
A single row of glia at the dorsal midline of the developing neural tube along the entire anterior-posterior axis. This region provides inductive signals for the specification of neuronal cell types and of the specification of neural crest cells. The cells comprising the roof plate are the precursors to radial glial cells.
TODO - Note that although this is classically defined as being located on the neural tube, in many AOs the roof plate continues post-embryonically after the neural tube has ceased to exist. Consider 'roof plate of neural tube'. TODO - alar plate vs roof plate
Multi-tissue structure that is the dorsal-most aspect of the devleloping neural tube.[TAO]
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
The hypochord is a transient rod-like structure in the embryos of fish, lampreys and amphibians that is located immediately ventral to the notochord. The hypochord may play a role in positioning the dorsal aorta[GO].
A transient rod-like structure which is endodermally derived and located immediately ventral to the notochord. The hypochord is thought to play a role in positioning the dorsal aorta. Eriksson and Lofberg, 2000.[TAO]
Unsegmented ventral structure in the caudal region of anuran larvae; near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle.[AAO]
In other words, we identified variations in gene expression patterns that may contribute to a molecular basis of evolutionary variation of axial structures between Teleostei and Mammalia in the determination of body axis. As already mentioned, one such difference is illustrated by the hypochord present in lower vertebrates but absent in higher animals. Perhaps, Tbx-b and Tbx-c are involved in the mechanisms underlying the formation of this organ that were lost during later evolution leading to the disappearance of the hypochord itself, similarly to other organs, such as the lateral line.[uncertain][VHOG]
Unlike in frogs and axolotl, the hypochord does not appear to be endodermally derived[ZFA]. near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle[AAO]
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]
The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
organizer for gastrulation in vertebrates. The primitive knot starts as a regional knot of cells that forms on the blastodisc immediately anterior to where the outer layer of cells will begin to migrate inwards - an area known as the primitive streak. Posterior to the node is the primitive pit, where the cells of the epiblast (the upper layer of embryonic cells) initially begin to invaginate. This invagination expands posteriorly into the primitive groove as the cells layers continue to move into the space between the embryonic cells and the yolk. This differentiates the embryo into the germ layers - endoderm, mesoderm, and ectoderm. The primitive knot migrates posteriorly as gastrulation proceeds, eventually being absorbed into the tail bud.[WP]. the regional thickening of cells at the rostral tip of the vertebrate primitive streak through which gastrulating cells migrate anteriorally to form tissues in the future head and neck; this region organizes the formation of the three embryonic layers and establishes the longitudinal axis and the polarity of the embryo[MP].
This class groups together possibly disparate structures, following homology class in vHOG; early development terms need review
A signaling center that directs the development of the whole embryo or of part of the embryo.[AAO]
Embryonic structure that is a local accumulation of cells along the germ ring. The shield marks the dorsal side of the embryo[ZFIN:ZDB-PUB-961014-576].
The organizer is a central feature of vertebrate embryogenesis. It was first characterized in functional terms in amphibians by Spemann and Mangold (1924), and homologous tissues have since been identified in representatives of most other vertebrate classes, including mammals (the node), birds (Henson's node) and teleost fish (the embryonic shield).[well established][VHOG]
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
TODO - check; developmental relationship to anterior hypoblast in ZFA?
check relationship to prechordal mesoderm. See http://www.ncbi.nlm.nih.gov/pubmed/16313393
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]
all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').
Region at the periphery of the retina where retinal stem cells are located. After 60 hpf, the CMZ is the source of most retinal growth.[Wehman et al, 2005]
Region at the periphery of the retina where retinal stem cells are located. After 60 hpf, the CMZ is the source of most retinal growth. Wehman et al, 2005.[TAO]
The retina of all vertebrates develops via similar mechanisms. Toward the end of retinal histogenesis, proliferating progenitors and newly generated cells are confined to peripheral regions of the retina. In fish and amphibians, this region is maintained after embryonic development and becomes the CMZ (ciliary margin zone). A CMZ exists in birds but compared to that of fish and amphibians this region produces much less new retina as the globe of the eye expands postnatally. At least some of the molecular mechanisms that regulate the addition of new cells in this zone appear to have been conserved from fish to birds.[well established][VHOG]
The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements.
The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
Lateral neurogenic placodes positioned dorsal of the epibranchial placodes.
In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]
Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991).
The ectodermal rudiment of the trigeminal ganglion.
The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]
The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]
The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
Fig9-5 of ISBN10:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].
TODO - mesonephric portion of the nephric duct
Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]
In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]
Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively
in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group
The specialized glial structure (non-neuronal cells) situated at the ventral midline of the embryonic neural tube; this structure spans the anteroposterior axis from the midbrain to the tail regions, separating the left and right basal plates of the developing neural tube, and serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube.
Organizing center consisting of a small group of cells located at the ventral midline of the neural tube that influences the development of the nervous system, governing the specification of neuronal cell types and directing axonal trajectories.[AAO]
although this is classically defined as being located on the neural tube, in many AOs the floor plate continues post-embryonically after the neural tube has ceased to exist. Consider 'floor plate of neural tube'.
A structure integral to the developing nervous system of vertebrate organisms. Located on the ventral midline of the embryonic neural tube, the floor plate is a specialized glial structure that spans the anteroposterior axis from the midbrain to the tail regions. It has been shown that the floor plate is conserved among vertebrates with homologous structures in invertebrates such as the fruit fly Drosophila and the nematode C. elegans. Functionally, the structure serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube.
TODO - add grouping class for the anterior end of the neural tube at all stages
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
The artery in vertebrate embryos that carries blood from the ventricle of the heart to the aortic arches. In adult fish it branches into afferent branchial arteries supplying the gills. In adult tetrapods it is represented by the ascending part of the aorta[BTO]. The ventral aorta is a blood vessel in a single-pass circulatory system that carries de-oxygenated blood from the heart to the gills. In a single-pass circulatory system blood passes once through the heart to supply the body once[GO].
Outflow artery from the heart to the aortic arches. Kimmel et al, 1995.[TAO]
Taxon notes (via vHOG): "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them." Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.620. // in Reptiles, splits to form bases of 3 arteries: left aortic arch, right aortic arch and pulmonary trunk. In birds, the right systemic arch becomes predominant, the left never fully develops [Kardong]
Extension of the dorsal aorta in the tail.
Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO]
The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO]
One of the the two paired cardinal veins draining the cephalic part of the body.
The anterior cardinal vein returns blood from the dorsal head and drains into the duct of Cuvier via the pronephric sinus.[AAO]
contribute to the formation of the internal jugular veins and together with the common cardinal vein form the superior vena cava. In an anastomosis by anterior cardinal veins, the left brachiocephalic vein is produced[WP]
Vein in the tail returning blood from the trunk and tail to the heart, leads directly into the posterial cardinal vein in the posterior trunk. Kimmel et al, 1995.[ZFIN]
Vein in the tail returning blood from the trunk and tail to the heart, leads directly into the posterial cardinal vein in the posterior trunk. Kimmel et al, 1995.[TAO]
Vein in the tail returning blood from the trunk and tail to the heart, leads directly into the posterior cardinal vein in the posterior trunk[XB:curator].
relationship loss: develops_from caudal vein plexus (TAO:0001286)[TAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
The lateral line that is located above the eye.
One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]
The lateral line that is located above the eye. [Butler_AB_and_Hodos_W, Comparative_vertebrate_neuroanatomy:_Evolution_and_Adaptation_(1996)_New_York:_Wiley-Liss_Inc., p.27][VHOG]
The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus.
Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator].
In all vertebrates the thyroid arises from the ventral aspect of the second pouch
Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm
An outpocketing of one of the caudal pharyngeal pouches that is comprised on calcitonin-producing parafollicular cells.
TODO - ensure developmental relationships correct across species. WP says pouch 4, but this isn't supported by Kardong (table 13.1 or fig 15.5). MP says 'fifth pouch in human or as the ventral component of the fourth pouch in mouse'. EHDAA2 says 6th arch mesenchyme http://www.ncbi.nlm.nih.gov/pubmed/16313389 says: the most posterior pouch generates the ultimobranchial bodies in most vertebrate classes, but mammals do not contain this structure
Anatomical structure which includes small, calcitonin producing glands originating as epithelial growths from the sixth pharyngeal pouch.[AAO]
The glandular tissue originating from the fifth branchial pouch which combines with the buccal cavity outgrowth to form the thyroid and contributes calcitonin-secreting cells to the gland. [TFD][VHOG]
(...) ultimobranchial bodies that develop in all vertebrates from the ventral or posterior surface of the last pair of pharyngeal pouches. The ultimobranchial bodies are vestigial in most mammals (...).[well established][VHOG]
In humans, the ultimobranchial body is an embryological structure that gives rise to the calcitonin-producing cells - also called parafollicular cells or clear cells - of the thyroid gland. In humans, this body is a derivative of the ventral recess of the fourth pharyngeal pouch (or fifth)
The ultimobranchial bodies of lower vertebrates contain large amounts of calcitonin. In mammals the bodies fuse with the thyroid gland and are thought to develop into the parafollicular cells. (Stedman, 25th ed)
The lateral line that is located below the eye.
The lateral line that is located below the eye. [Butler_AB_and_Hodos_W, Comparative_vertebrate_neuroanatomy:_Evolution_and_Adaptation_(1996)_New_York:_Wiley-Liss_Inc., p.27][VHOG]
A lateral line that is located in the dorsal part of the organism.
relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO]
relationship loss: develops_from middle lateral line primordium (TAO:0005118)[TAO]
relationship loss: part_of middle lateral line system (TAO:0005114)[TAO]
Median fin located on the dorsal surface of the organism.
the narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain
The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
Gonochoristic organism that can produce female gametes.
Gonochoristic organism that can produce male gametes.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
Curator notes: this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Region located near the pronephros and pronephric ducts that is a site of hematopoiesis in the embryo.
Region located near the pronephros and pronephric ducts that is a site of hematopoiesis in the embryo.[AAO]
Region where blood progenitor markers are expressed. Probable site of definitive hematopoiesis between 36hpf and 4dpf.[TAO]
In teleosts: Anatomical cluster that is the result of fusion of preural centrum 1 with one or more adjacent ural centra[AAO]; Rodlike caudal bony structure unique to anurans that lies within a compartment formed by the elongated, anteriorly oriented pelvic girdle. The urostyle is formed by the fusion of the coccyx and the hypochord[AAO].
Anatomical cluster that is the result of fusion of preural centrum 1 with one or more adjacent ural centra.[TAO]
Rodlike caudal bony structure unique to anurans that lies within a compartment formed by the elongated, anteriorly oriented pelvic girdle. The urostyle is formed by the fusion of the coccyx and the hypochord.[AAO]
relationship loss: part_of caudal fin skeleton (VSAO:0000167)[TAO]
In zebrafish, it is composed of preural vertebra 1 and ural centra 1 and 2. The number of ural centra that become fused with preural centrum 1 varies among teleost subgroups. Because of varying developmental origins the urostyle may not be homologous across species.[TAO]
In zebrafish, it is composed of preural vertebra 1 and ural centra 1 and 2. The number of ural centra that become fused with preural centrum 1 varies among teleost subgroups. Because of varying developmental origins the urostyle may not be homologous across species.
Meckel's cartilage is the bilaterally paired, rod-like, cartilaginous ventral component of the lower jar, or ventral mandibular arch. It is typically resorbed in adults.
Paired, rod-shaped elements that extend the length of the mandible and lie between the dentaries and the angulosplenials. Can be reduced to various extent in adults.[AAO]
Pharyngeal arch cartilage that is the cartilaginous embryonic component of the lower jaw, or ventral mandibular arch. It develops into the endochondral articular and retroarticular bones. Meckel's cartilage is paired.[TAO]
In all jawed vertebrates, including fish, the first pharyngeal arch generates the jaw apparatus. The neural crest cells of this arch migrate to form Meckel's cartilage, the precursor of the jaw.[well established][VHOG]
functional lower jaw of Elasmobranchii and Holocephali, the embryonic lower jaw of other gnathostomous vertebrates
(1) the arrangement of bones which supports the jaw from the braincase; (2) in teleost fish, a large, usually triangular, bone which supports the jaw. The teleost suspensorium is formed by fusion of various elements which vary among different taxa.
requires review, possible split; TAO/ZFA structure is splanchoncranium (but includes some dermal bones as parts). Note AAO also includes 'palatoquadrate and suspensorium' as a class
Endochondral bone that forms from a lateral outgrowth of the basiventral arcualia and connects the rib with the vertebral centrum[TAO]. A lateral or ventrolateral projections of vertebrae to which ribs are attached in Danio rerio. ZFA: They can arise through replacement ossification of a basiventral or form directly in bone. They are separated from the centrum in basal teleosts, e.g., Leptolepis coryphaenoides, Megalops and Elops.
Endochondral bone that forms from a lateral outgrowth of the basiventral arcualia and connects the rib with the vertebral centrum.[TAO]
Paired processes, which arise near the dorsolateral part of the vertebral centrum, for the attachment of the capitulum of two-headed ribs.[AAO]
Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae.[AAO]
relationship loss: develops_from basiventral (TAO:0001361)[TAO]
relationship loss: part_of non-Weberian precaudal vertebra (TAO:0001582)[TAO]
Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO]
Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO]
relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO]
UBERONREF:0000007 has this as a syn for otic capsule
Anatomical cluster that forms the floor and sidewalls of the middle part of the cranium.
Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO]
Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ.
Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO]
Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO]
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus.
The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO]
in XAO, called branchial arch 1 and df VP3
contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus
The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]
in XAO, called branchial arch 2 and df VP4
The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
A fifth arch never establishes itself in amniotes
in XAO, called branchial arch 3 and df VP5
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
The vessels formed within the first pair of branchial arches in embryogenesis
Disappears early in development in tetrapods
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
The vessels formed within the second pair of branchial arches in embryogenesis
The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2].
The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO]
The vessels formed within the third pair of branchial arches in embryogenesis
Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]
The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3].
The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The vessels formed within the fourth pair of branchial arches in embryogenesis
The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4].
Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta
The vessels formed within the fifth pair of pharyngeal arches in embryogenesis.
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5].
The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO]
In humans the 5th arch disappears on both sides
The vessels formed within the sixth pair of branchial arches in embryogenesis
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]
The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252].
The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN10:0073040584]
A structure directly adjacent to the outer surface of the plasma membrane of an ovum. It is composed mostly of protein fibers, with protein receptors needed for sperm binding, binding to sperm plasma membrane receptors. The species-specificity between these receptors contributes to prevention of breeding between different species [Wikipedia]. A protective layer around the egg[FBbt].
TODO - consider GO CC request. GO:0030704-vitelline membrane formation considered a subclass of CC organization
Thin membrane enclosing and immediately adjacent to the ovum. Produced in the ovary.[AAO]
relationship loss: part_of zygote (AAO:0010324)[AAO]
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
An elongated tube which carries air to and from the lungs.[AAO]
The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]
In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx.
A respiratory airway that is part of an open tracheal system.
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
ventral portion of a segment of an arthropod thorax or abdomen. In insects, the sterna are usually single, large sclerites, and external. However, they can sometimes be divided in two or more, in which case the subunits are called sternites, and may also be modified on the terminal abdominal segments so as to form part of the functional genitalia, in which case they are frequently reduced in size and development, and may become internalized and/or membranous.
homology of leg segments between groups are difficult to prove and are the source of much argument. Some authors posit up to eleven segments per leg for the most recent common ancestor of extant arthropods, but modern arthropods have eight or fewer.
that the ancestral leg need not have been so complex, and that other events, such as the successive loss of function of a Hox-gene could result in parallel gains of leg segments.
A median tonguelike structure arising from the mouth.
GO uses genitalia for the singular organ
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
reproductive system organ of male organism
arthropod specific groupings belong in separate ontology
An organism at the prepupal stage. The prepupal stage is a life stage interposed between the larval and the pupal stages in insects that undergo a complete metamorphosis. The start of the pre-pupal stage is marked by pupariation, and the end is marked by pupation
An organism at the pupal stage. A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
That part of the integument of an insect which surrounds the spiracles.
arthropod specific groupings belong in separate ontology. term also used for edge of the aperture of a univalve shell
hardened portions of arthropod exoskeletons.
The lamella that serves as the site of attachment of the longitudinal flight muscle [HAO].
arthropod specific groupings belong in separate ontology, but this is retained for disambiguation purposes
A simple visual organ of insects[GO]. Two ocelli appear on the vertical and one on the frontal plate[FBbt]. The multi-tissue structure that is located on the top of the head, composed of the corneal lens, pigment cell, rhabdoms and synaptic plexus[HAO]. Two evolutionary distinct ocellus types exist [2]: dorsal ocelli (or simply 'ocelli'), found in most insects, and lateral ocelli (or stemmata), which are found in the larvae of some insect orders. They are structurally and functionally very different. Simple eyes of other animals, e.g. cnidarians may also be referred to as 'ocelli', but again the structure and anatomy of these eyes is quite distinct from those of the dorsal ocelli of insects[Wikipedia].
The ocellus that is paired[HAO]. The number, form, and function of the dorsal ocelli varies markedly throughout insect orders. They tend to be larger and more strongly expressed in flying insects (particularly bees, wasps, dragonflies and locusts), where they are typically found as a triplet. Two lateral ocelli are directed to the left and right of the head respectively, while a central (median) ocellus is directed frontally. In some terrestrial insects (e.g. some ants and cockroaches), only two lateral ocelli are present: the median ocellus is absent. Note that the unfortunately labelled 'lateral ocelli' here refers to the sideways facing position of the ocelli, which are of the dorsal type. They should not be confused with the lateral ocelli of some insect larvae (see stemmata)[Wikipedia].
The outer layer of the procuticle of certain crustaceans and arthropods, which contains cuticulin, chitin, and phenolic substances that are oxidized to produce the dark pigment of the cuticle;nThe hard and usually darkened layer of the cuticle lying between the endocuticle and epicuticle.
The inner layer of the procuticle in certain crustaceans and arthropods, which is almost entirely composed of protein and chitin.
Uberon now includes a generic appendicular segment class. Note the HAO class for appendage segment has been obsoleted
barrier between the perineurium of peripheral nerves and the vascular endothelium of endoneurial capillaries. The perineurium acts as a diffusion barrier, but ion permeability at the blood-nerve barrier is still higher than at the blood-brain barrier[GO].
barrier in the choroid plexus located in the lateral, third, and fourth brain ventricles that controls the entrance of substances into the cerebrospinal fluid from the blood[MP].
A median eye is an ➞eye that is connected to a paired or unpaired median anterior ➞neuropil of the ➞syncerebrum by one or several median eye nerves.
Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912).
A sac-like structure that is found in the mature gland[GO].
organ part that has the form of a hollow cavity[WP].
Anterior portion of the palate consisting of bone and mucous membranes[GO]. The hard palate is formed from bony processes of the maxilla, premaxilla and palatine[Kardong].
in FMA this is divided into bony parts and submucosa
The posterior pituitary (or neurohypophysis) comprises the posterior lobe of the pituitary gland and is part of the endocrine system. Despite its name, the posterior pituitary gland is not a gland, per se; rather, it is largely a collection of axonal projections from the hypothalamus that terminate behind the anterior pituitary gland. [WP,unvetted].
pars nervosa of posterior lobe of pituitary gland
Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO].
Septum that divides the internal chambers (camerae) of the shell of a cephalopod, namely nautiloids or ammonoids.
one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]
A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]
When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.
In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three
An extrinsic flexor muscle of the fingers at the proximal interphalangeal joints.[WP].
An extraembryonic structure that develops_from a syncytiotrophoblast and is part of a chorion.
A muscle which originates on the distal humerus, inserts on the radius and accomplishes supination (rotation of the wrist).
TODO - The term 'supinator' can also refer more generally to a muscle that causes supination of a part of the body. In older texts, the term 'supinator longus' was used to refer to the brachioradialis, and 'supinator brevis' was used to the muscle now known as the supinator.
An epithelium that is part of a elbow [Automatically generated definition].
An epithelium that is part of a wrist [Automatically generated definition].
An epithelium that is part of a hip [Automatically generated definition].
An epithelium that is part of a knee [Automatically generated definition].
An epithelium that is part of a shoulder [Automatically generated definition].
The Extensor pollicis longus is much larger than the Extensor pollicis brevis muscle, the origin of which it partly covers.
An epithelium that is part of a upper jaw [Automatically generated definition].
epithelial tissue of palatoquadrate arch
An epithelium that is part of a lower jaw [Automatically generated definition].
epithelial tissue of ventral mandibular arch
ventral mandibular arch epithelial tissue
An epithelium that is part of an anterior semicircular canal [Automatically generated definition].
anterior semicircular canal epithelial tissue
epithelial tissue of anterior semicircular canal
epithelial tissue of superior semicircular canal
epithelium of anterior semicircular canal
superior semicircular canal epithelial tissue
epithelium of superior semicircular canal
An epithelium that is part of a posterior semicircular canal [Automatically generated definition].
epithelial tissue of posterior semicircular canal
posterior semicircular canal epithelial tissue
epithelium of posterior semicircular canal
An epithelium that is part of a lateral semicircular canal [Automatically generated definition].
epithelial tissue of lateral semicircular canal
lateral semicircular canal epithelial tissue
epithelium of lateral semicircular canal
An epithelium that is part of a utricle of membranous labyrinth [Automatically generated definition].
epithelial tissue of membranous labyrinth utricle
epithelial tissue of utricle of membranous labyrinth
epithelial tissue of utriculus (labyrinthus vestibularis)
epithelium of membranous labyrinth utricle
epithelium of utricle of membranous labyrinth
epithelium of utriculus (labyrinthus vestibularis)
membranous labyrinth utricle epithelial tissue
utricle of membranous labyrinth epithelial tissue
utricle of membranous labyrinth epithelium
utriculus (labyrinthus vestibularis) epithelial tissue
utriculus (labyrinthus vestibularis) epithelium
epithelium of macula of utricle of membranous labyrinth
An epithelium that is part of a saccule of membranous labyrinth [Automatically generated definition].
epithelial tissue of membranous labyrinth saccule
epithelial tissue of saccule of membranous labyrinth
epithelial tissue of sacculus (labyrinthus vestibularis)
epithelium of membranous labyrinth saccule
epithelium of saccule of membranous labyrinth
epithelium of sacculus (labyrinthus vestibularis)
membranous labyrinth saccule epithelial tissue
saccule of membranous labyrinth epithelial tissue
saccule of membranous labyrinth epithelium
sacculus (labyrinthus vestibularis) epithelial tissue
sacculus (labyrinthus vestibularis) epithelium
epithelium of macula of saccule of membranous labyrinth
An epithelium that is part of a cochlear duct of membranous labyrinth [Automatically generated definition].
cochlear duct of membranous labyrinth epithelial tissue
cochlear duct of membranous labyrinth epithelium
epithelial tissue of cochlear duct of membranous labyrinth
epithelium of cochlear duct of membranous labyrinth
the epithelial layer of the luminal surfaces of the mammary gland
An epithelium that is part of a endolymphatic sac [Automatically generated definition].
An epithelium that is part of a lower arm [Automatically generated definition].
arm middle limb segment epithelial tissue
brachial region middle limb segment epithelial tissue
brachial region middle limb segment epithelium
brachial region zeugopod epithelial tissue
epithelial tissue of antebrachial region
epithelial tissue of arm middle limb segment
epithelial tissue of brachial region middle limb segment
epithelial tissue of brachial region zeugopod
epithelial tissue of intermediate segment of free upper limb
epithelial tissue of lower segment of arm
epithelial tissue of middle limb segment of arm
epithelial tissue of middle limb segment of brachial region
epithelial tissue of middle limb segment of proximal segment of free upper limb
epithelial tissue of proximal segment of free upper limb middle limb segment
epithelial tissue of proximal segment of free upper limb zeugopod
epithelial tissue of zeugopod of brachial region
epithelial tissue of zeugopod of proximal segment of free upper limb
epithelium of brachial region middle limb segment
epithelium of intermediate segment of free upper limb
epithelium of middle limb segment of arm
epithelium of middle limb segment of brachial region
epithelium of middle limb segment of proximal segment of free upper limb
epithelium of proximal segment of free upper limb middle limb segment
epithelium of proximal segment of free upper limb zeugopod
epithelium of zeugopod of brachial region
epithelium of zeugopod of proximal segment of free upper limb
intermediate segment of free upper limb epithelial tissue
intermediate segment of free upper limb epithelium
middle limb segment of arm epithelial tissue
middle limb segment of brachial region epithelial tissue
middle limb segment of brachial region epithelium
middle limb segment of proximal segment of free upper limb epithelial tissue
middle limb segment of proximal segment of free upper limb epithelium
proximal segment of free upper limb middle limb segment epithelial tissue
proximal segment of free upper limb middle limb segment epithelium
proximal segment of free upper limb zeugopod epithelial tissue
proximal segment of free upper limb zeugopod epithelium
zeugopod of brachial region epithelial tissue
zeugopod of proximal segment of free upper limb epithelial tissue
zeugopod of proximal segment of free upper limb epithelium
An epithelium that is part of a footplate.
An epithelium that is part of a otic placode [Automatically generated definition].
check ZFA, placemeant, appears to refer to both adult structures and primordium
A muscle that arises from the upper surface of the transverse process of the atlas and inserts into the under surface of the jugular process of the occipital bone.
Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case.
Anatomical cluster that consists of more than one rib in an individual.[TAO]
The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs.
we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.
deleted because the original definition was unclear. Me may reconstitute this and to distinguish extramebryonic from embryonic germ layers. See amniotic ectoderm and amniotic mesoderm
An extraembryonic structure that develops_from a endoderm and is part of a yolk sac.
An endoderm that is part of a foregut [Automatically generated definition].
An endoderm that is part of a midgut [Automatically generated definition].
An endoderm that is part of a hindgut [Automatically generated definition].
An endoderm that is part of a thyroid primordium.
A mesoderm that is part of a yolk sac [Automatically generated definition].
obsoleted pending formal definition of nerve, with explicit reference to PNS vs CNS. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
obsolete nerve of central nervous system
A calcareous tooth that is part of the upper jaw region. In mammals, the upper jaw teeth are attached to the maxilla.
Note that we follow EHDAA2 and consider teeth part of the jaw skeleton
A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary).
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a tongue [Automatically generated definition].
consider merging with 'muscle of tongue', depending on outcome of issue 331
A mesothelium that is part of a lesser sac [Automatically generated definition].
A skeletal system that is part of a embryo [Automatically generated definition].
developmental tissue set of bones of body
set of all bones of developmental tissue
set of bones of body of developmental tissue
A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones.
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
EMAPA/MA placement unclear. See https://sourceforge.net/p/obo/mouse-anatomy-requests/88/
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: develops_from anatomical cluster (UBERON:0000477)[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: overlaps anatomical cluster (UBERON:0000477)[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: part_of anatomical cluster (UBERON:0000477)[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: subdivision_of anatomical cluster (UBERON:0000477)[TAO]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://sourceforge.net/p/obo/mouse-anatomy-requests/88/
An endothelium that is part of a trachea.
An endothelium that is part of a main bronchus [Automatically generated definition].
The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum.
The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]
A mesentery that is part of a esophagus [Automatically generated definition].
A mesentery that is part of a midgut [Automatically generated definition].
A meninx that is part of a midbrain [Automatically generated definition].
consider changing genus to subdivision of meninx
Meninges that are part of the midbrain. [Bgee_curator][VHOG]
A meninx that is part of a telencephalon [Automatically generated definition].
Meninges that are part of the telencephalon. [Bgee_curator][VHOG]
A meninx that is part of a diencephalon [Automatically generated definition].
Meninges that are part of the diencephalon. [Bgee_curator][VHOG]
A meninx that is part of a hindbrain [Automatically generated definition].
Meninges that are part of the hindbrain. [Bgee_curator][VHOG]
A meninx that is part of a spinal cord [Automatically generated definition].
Meninges that are part of the spinal cord. [Bgee_curator][VHOG]
A gland that is part of a foregut [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis.
A gland that is part of a integumental system [Automatically generated definition].
A roof plate that is part of a neural tube [Automatically generated definition].
the mesencephalic roof plate, including the caudal and rostral part of the midbrain roof
Roof plate that is part of the midbrain. [Bgee_curator][VHOG]
A roof plate that is part of a telencephalon [Automatically generated definition].
Roof plate that is part of the telencephalon. [Bgee_curator][VHOG]
A roof plate that is part of a diencephalon [Automatically generated definition].
Roof plate that is part of the diencephalon. [Bgee_curator][VHOG]
A roof plate that is part of a metencephalon [Automatically generated definition].
Roof plate that is part of the metencephalon. [Bgee_curator][VHOG]
A roof plate that is part of a medulla oblongata [Automatically generated definition].
Roof plate that is part of the medulla oblongata. [Bgee_curator][VHOG]
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
A floor plate that is part of a neural tube [Automatically generated definition].
In summary, the available data for tunicates, amphioxus, and vertebrates indicate that a floorplate-like structure was already present in the proximate invertebrate ancestor of the vertebrates and that the genetic mechanisms for DV patterning of the nerve cord were also largely in place.[well established][VHOG]
although 'floor plate' is classically defined as being located on the neural tube, in many AOs the floor plate continues post-embryonically after the neural tube has ceased to exist. We introduce this class for the neural tube specific structure
A floor plate that is part of a midbrain [Automatically generated definition].
Floor plate that is part of the midbrain.[TAO]
relationship type change: subclass multi-tissue structure (CARO:0000055) CHANGED TO: develops_from multi-tissue structure (UBERON:0000481)[TAO]
relationship type change: subclass multi-tissue structure (CARO:0000055) CHANGED TO: part_of multi-tissue structure (UBERON:0000481)[TAO]
A floor plate that is part of a telencephalon [Automatically generated definition].
A floor plate that is part of a diencephalon [Automatically generated definition].
A floor plate that is part of a metencephalon [Automatically generated definition].
A floor plate that is part of a medulla oblongata [Automatically generated definition].
Mesenchyme that is part of a developing testis [Automatically generated definition].
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
Mesenchyme that is part of a developing ovary [Automatically generated definition].
female reproductive system gonad mesenchyme
female reproductive system gonada mesenchyme
gonad of female reproductive system mesenchyme
gonada of female reproductive system mesenchyme
mesenchyme of female reproductive system gonad
mesenchyme of female reproductive system gonada
mesenchyme of gonad of female reproductive system
mesenchyme of gonada of female reproductive system
Mesenchyme that is part of a yolk sac [Automatically generated definition].
An odontogenic papilla that is part of a incisor tooth [Automatically generated definition].
Mesenchyme that is part of a developing elbow [Automatically generated definition].
Mesenchyme of the carpal region that conributes to the carpal skeleton.
Mesenchyme that is part of a developing hip [Automatically generated definition].
Mesenchyme that is part of a developing knee [Automatically generated definition].
Mesenchyme that is part of a developing shoulder [Automatically generated definition].
Mesenchyme that is part of a developing upper jaw [Automatically generated definition].
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
Mesenchyme that is part of a developing pinna [Automatically generated definition].
Mesenchyme that is part of a developing mammary gland.
Mesenchyme that is part of a developing lower arm [Automatically generated definition].
brachial region middle limb segment mesenchyme
intermediate segment of free upper limb mesenchyme
mesenchyme of brachial region middle limb segment
mesenchyme of intermediate segment of free upper limb
mesenchyme of middle limb segment of arm
mesenchyme of middle limb segment of brachial region
mesenchyme of middle limb segment of proximal segment of free upper limb
mesenchyme of proximal segment of free upper limb middle limb segment
mesenchyme of proximal segment of free upper limb zeugopod
mesenchyme of zeugopod of brachial region
mesenchyme of zeugopod of proximal segment of free upper limb
middle limb segment of brachial region mesenchyme
middle limb segment of proximal segment of free upper limb mesenchyme
proximal segment of free upper limb middle limb segment mesenchyme
proximal segment of free upper limb zeugopod mesenchyme
zeugopod of proximal segment of free upper limb mesenchyme
A submucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically submucosa
submucosa of anal canal viewed anatomically
The submucous layer of the wall of the rectum.
A submucosa that is part of a colon [Automatically generated definition].
A submucosa that is part of a duodenum [Automatically generated definition].
A submucosa that is part of a jejunum [Automatically generated definition].
A serous membrane that is part of a rectum [Automatically generated definition].
A serous membrane that is part of a colon [Automatically generated definition].
A serous membrane that is part of a duodenum [Automatically generated definition].
A serous membrane that is part of a jejunum [Automatically generated definition].
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
A ganglion that is part of a central nervous system [Automatically generated definition].
this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia
A mucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically mucosa of organ
anal canal viewed anatomically mucous membrane
anal canal viewed anatomically organ mucosa
mucosa of anal canal viewed anatomically
mucosa of organ of anal canal viewed anatomically
mucosa of organ of anatomical anal canal
mucous membrane of anal canal viewed anatomically
mucous membrane of anatomical anal canal
organ mucosa of anal canal viewed anatomically
A mucosa that is part of a oral opening [Automatically generated definition].
A mucosa that is part of a rectum [Automatically generated definition].
A layer of epithelial cells on the surface of the mucosa.
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
An epithelium that is part of a hindgut [Automatically generated definition].
An epithelium that is part of a rectum [Automatically generated definition].
An epithelium that is part of a incisor tooth [Automatically generated definition].
An epithelium that is part of a nasal septum [Automatically generated definition].
An epithelium that is part of a tongue [Automatically generated definition].
examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies.
An epithelium that is part of a soft palate [Automatically generated definition].
An epithelium that is part of a submandibular gland [Automatically generated definition].
epithelial tissue of submandibular gland
An epithelium that is part of a parotid gland [Automatically generated definition].
An epithelium that is part of a sublingual gland [Automatically generated definition].
epithelial tissue of ductus sublingualis
An epithelium that is part of a endolymphatic duct [Automatically generated definition].
An epithelium that is part of a ductus reuniens [Automatically generated definition].
An epithelium that is part of a right lung [Automatically generated definition].
An epithelium that is part of a left lung [Automatically generated definition].
An epithelium that is part of a uterine horn [Automatically generated definition].
An epithelium that is part of a vomeronasal organ [Automatically generated definition].
An epithelium that is part of a hard palate [Automatically generated definition].
Found in the right atrium of the heart, the fossa ovalis is an embryonic remnant of the foramen ovale, which normally closes shortly after birth. In a heart specimen of a neonate, the fossa ovalis is translucent, but later in life the membrane thickens.
An unilaminar epithelium that surrounds a pelvic appendage bud.
An unilaminar epithelium that surrounds a pectoral appendage bud.
An ectoderm that is part of a footplate.
A extraembryonic structure that develops_from a ectoderm and is part of a chorion.
A cardiac muscle tissue that is part of a atrium auricular region.
A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition].
cardiac muscle tissue of heart right atrium
cardiac muscle tissue of right atrium of heart
textus muscularis of myocardium of right atrium
textus muscularis of myocardium of right atrium of heart
textus muscularis of myocardium of right cardiac atrium
A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition].
cardiac left atrium cardiac muscle tissue
textus muscularis of myocardium of cardiac left atrium
textus muscularis of myocardium of heart left atrium
textus muscularis of myocardium of left atrium
textus muscularis of myocardium of left atrium of heart
textus muscularis of myocardium of left cardiac atrium
A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of right ventricle
A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition].
cardiac muscle of interventricular septum
cardiac muscle tissue of interventricular septum
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition].
A mesothelium that is part of a pericardium [Automatically generated definition].
cavity of pericardial sac meso-epithelium
meso-epithelium of cavity of pericardial sac
mesothelium of cavity of pericardial sac
A mesothelium that is part of a diaphragm [Automatically generated definition].
A mesothelium that is part of a pleural cavity [Automatically generated definition].
A mesentery that is part of a urinary system [Automatically generated definition].
A mesentery that is part of a hindgut [Automatically generated definition].
A mesentery that is part of a rectum [Automatically generated definition].
A mesentery that is part of a colon [Automatically generated definition].
A mesentery that is part of a duodenum [Automatically generated definition].
A mesentery that is part of a jejunum [Automatically generated definition].
A zone of skin that is part of a lower arm [Automatically generated definition].
brachial region middle limb segment skin
intermediate segment of free upper limb skin
middle limb segment of brachial region skin
middle limb segment of proximal segment of free upper limb skin
proximal segment of free upper limb middle limb segment skin
proximal segment of free upper limb zeugopod skin
skin of brachial region middle limb segment
skin of intermediate segment of free upper limb
skin of middle limb segment of brachial region
skin of middle limb segment of proximal segment of free upper limb
skin of proximal segment of free upper limb middle limb segment
skin of proximal segment of free upper limb zeugopod
skin of zeugopod of proximal segment of free upper limb
zeugopod of proximal segment of free upper limb skin
A lobar bronchus that is part of a right lung [Automatically generated definition].
A lobar bronchus that is part of a left lung [Automatically generated definition].
A cartilage element that is part of a respiratory system [Automatically generated definition].
A cartilage that is part of a nasal septum [Automatically generated definition].
A gland that is part of a digestive tract [Automatically generated definition].
Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue.
A gland that is part of a oropharynx [Automatically generated definition].
Mesenchyme that is part of a pelvic appendage bud.
Mesenchyme that is part of a pectoral appendage bud.
Mesoderm that is part of the pectoral fin bud.[TAO]
Mesenchyme that is part of a developing mandible [Automatically generated definition].
bone of ventral mandibular arch mesenchyme
bone organ of ventral mandibular arch mesenchyme
mesenchyme of bone of ventral mandibular arch
mesenchyme of bone organ of ventral mandibular arch
mesenchyme of ventral mandibular arch bone
mesenchyme of ventral mandibular arch bone organ
ventral mandibular arch bone organ mesenchyme
Mesenchyme that is part of a developing nasal septum [Automatically generated definition].
Mesenchyme that is part of a developing tongue [Automatically generated definition].
Mesenchyme that is part of a developing soft palate [Automatically generated definition].
Mesenchyme that is part of a developing submandibular gland [Automatically generated definition].
Mesenchyme that is part of a developing parotid gland [Automatically generated definition].
Mesenchyme that is part of a developing sublingual gland [Automatically generated definition].
Mesenchyme that is part of a developing vomeronasal organ [Automatically generated definition].
A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]
Mesenchyme that is part of a developing hard palate [Automatically generated definition].
A lymph node that is located in a kidney [Automatically generated definition].
Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland
An adipose tissue that is part of a dermis [Automatically generated definition].
The encapsulated adipose tissue in the abdomen.
The encapsulated adipose tissue associated with the ovaries or testes.
consider change relationship from part_of
Anatomical structure associated with the gonads which vary in form among amphibians but are primarily composed of adipose tissue and are thought to be a source of nutrients for the gonads.[AAO]
we place the amphibian structures here as their definitions state a gonadal association.
A nerve that is part of an abdomen [Automatically generated definition].
A nerve that is part of a neck [Automatically generated definition].
A nerve that is part of a leg [Automatically generated definition].
A nerve that is part of a chest [Automatically generated definition].
A nerve that is part of an arm [Automatically generated definition].
nerve of proximal segment of free upper limb
proximal segment of free upper limb nerve
A nerve that is part of a wrist [Automatically generated definition].
A nerve that is part of a toe [Automatically generated definition].
digit of terminal segment of free lower limb nerve
nerve of digit of terminal segment of free lower limb
nerve of terminal segment of free lower limb digit
terminal segment of free lower limb digit nerve
A nerve that is part of a shoulder [Automatically generated definition].
A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk).
A nerve that is part of a limb [Automatically generated definition].
A nerve that is part of a forelimb [Automatically generated definition].
A nerve that is part of a hindlimb [Automatically generated definition].
A nerve that is located in a thoracic cavity [Automatically generated definition].
consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
A nerve that is part of a pelvis [Automatically generated definition].
A nerve that is part of a foot [Automatically generated definition].
distal free limb segment of hind limb nerve
distal free limb segment of hindlimb nerve
distal free limb segment of inferior member nerve
distal free limb segment of lower extremity nerve
hind limb distal free limb segment nerve
inferior member distal free limb segment nerve
lower extremity distal free limb segment nerve
nerve of distal free limb segment of hind limb
nerve of distal free limb segment of hindlimb
nerve of distal free limb segment of inferior member
nerve of distal free limb segment of lower extremity
nerve of hind limb distal free limb segment
nerve of hindlimb distal free limb segment
nerve of inferior member distal free limb segment
nerve of lower extremity distal free limb segment
nerve of terminal segment of free lower limb
terminal segment of free lower limb nerve
A nerve that is part of an ankle [Automatically generated definition].
A nerve that is part of a finger [Automatically generated definition].
digit of terminal segment of free upper limb nerve
nerve of digit of terminal segment of free upper limb
nerve of terminal segment of free upper limb digit
terminal segment of free upper limb digit nerve
A nerve that is part of a manus [Automatically generated definition].
autopod of proximal segment of free upper limb nerve
brachial region distal free limb segment nerve
distal free limb segment of brachial region nerve
distal free limb segment of proximal segment of free upper limb nerve
nerve of autopod of proximal segment of free upper limb
nerve of brachial region distal free limb segment
nerve of distal free limb segment of arm
nerve of distal free limb segment of brachial region
nerve of distal free limb segment of proximal segment of free upper limb
nerve of proximal segment of free upper limb autopod
nerve of proximal segment of free upper limb distal free limb segment
nerve of terminal segment of free upper limb
proximal segment of free upper limb autopod nerve
proximal segment of free upper limb distal free limb segment nerve
terminal segment of free upper limb nerve
An intervertebral disk that is part of a tail [Automatically generated definition].
An incisor tooth that is part of a upper jaw [Automatically generated definition].
An incisor tooth that is part of a lower jaw [Automatically generated definition].
incisor tooth of ventral mandibular arch
A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition].
cardiac muscle muscle tissue of trabecula carnea
cardiac muscle textus muscularis of trabecula carnea
cardiac muscle tissue of trabecula carnea
heart muscle muscle tissue of trabecula carnea
heart muscle textus muscularis of trabecula carnea
heart myocardium muscle tissue of trabecula carnea
heart myocardium textus muscularis of trabecula carnea
muscle of heart muscle tissue of trabecula carnea
muscle of heart textus muscularis of trabecula carnea
muscle tissue of cardiac muscle of trabecula carnea
muscle tissue of heart muscle of trabecula carnea
muscle tissue of heart myocardium of trabecula carnea
muscle tissue of muscle of heart of trabecula carnea
muscle tissue of myocardium of trabecula carnea
myocardium muscle tissue of trabecula carnea
myocardium textus muscularis of trabecula carnea
textus muscularis of cardiac muscle of trabecula carnea
textus muscularis of heart muscle of trabecula carnea
textus muscularis of heart myocardium of trabecula carnea
textus muscularis of muscle of heart of trabecula carnea
textus muscularis of myocardium of trabecula carnea
trabecula carnea cardiac muscle muscle tissue
trabecula carnea cardiac muscle textus muscularis
trabecula carnea heart muscle muscle tissue
trabecula carnea heart muscle textus muscularis
trabecula carnea heart myocardium muscle tissue
trabecula carnea heart myocardium textus muscularis
trabecula carnea muscle of heart muscle tissue
trabecula carnea muscle of heart textus muscularis
trabecula carnea muscle tissue of cardiac muscle
trabecula carnea muscle tissue of heart muscle
trabecula carnea muscle tissue of heart myocardium
trabecula carnea muscle tissue of muscle of heart
trabecula carnea muscle tissue of myocardium
trabecula carnea myocardium muscle tissue
trabecula carnea myocardium textus muscularis
trabecula carnea textus muscularis of cardiac muscle
trabecula carnea textus muscularis of heart muscle
trabecula carnea textus muscularis of heart myocardium
trabecula carnea textus muscularis of muscle of heart
trabecula carnea textus muscularis of myocardium
A Peyer's patch that is part of a large intestine.
solitary lymphatic follicle of large intestine
solitary lymphoid follicle of subdivision of large intestine
nodular lymphoid structures on the serosal surface of the small intestine.
aggregated lymphoid follicle of small intestine
noduli lymphoidei aggregati intestini tenuis
A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition].
Henle loop of inner zone of medulla of kidney
Henle loop of inner zone of renal medulla
henle's loop of inner zone of medulla of kidney
henle's loop of inner zone of renal medulla
inner zone of medulla of kidney Henle loop
inner zone of medulla of kidney henle's loop
inner zone of medulla of kidney loop of Henle
inner zone of renal medulla henle's loop
inner zone of renal medulla loop of Henle
loop of Henle of inner medulla of kidney
loop of Henle of inner zone of medulla of kidney
loop of Henle of inner zone of renal medulla
A lymphatic vessel that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lymphatic vessel
lymphatic vessel of apparatus respiratorius
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a neck [Automatically generated definition].
A bone that is part of a chest [Automatically generated definition].
bone organ of anterolateral part of thorax
A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia
bone of proximal segment of free upper limb
bone organ of proximal segment of free upper limb
proximal segment of free upper limb bone
proximal segment of free upper limb bone organ
A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods.
this is a forelimb bone in MA, but this would lead to part-disjointness violations.
A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
A bone that is part of a trunk [Automatically generated definition].
A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)
the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc
A bone that is part of a chondrocranium [Automatically generated definition].
Made obsolete because it conflated neuro and chondro-cranium; also ZFA:0001544 equivalent was made obsolete.
A bone that is part of a lower arm [Automatically generated definition].
bone of brachial region middle limb segment
bone of intermediate segment of free upper limb
bone of middle limb segment of brachial region
bone of middle limb segment of proximal segment of free upper limb
bone of proximal segment of free upper limb middle limb segment
bone of proximal segment of free upper limb zeugopod
bone of zeugopod of proximal segment of free upper limb
bone organ of brachial region middle limb segment
bone organ of intermediate segment of free upper limb
bone organ of middle limb segment of arm
bone organ of middle limb segment of brachial region
bone organ of middle limb segment of proximal segment of free upper limb
bone organ of proximal segment of free upper limb middle limb segment
bone organ of proximal segment of free upper limb zeugopod
bone organ of zeugopod of brachial region
bone organ of zeugopod of proximal segment of free upper limb
brachial region middle limb segment bone
brachial region middle limb segment bone organ
intermediate segment of free upper limb bone
intermediate segment of free upper limb bone organ
middle limb segment of brachial region bone
middle limb segment of brachial region bone organ
middle limb segment of proximal segment of free upper limb bone
middle limb segment of proximal segment of free upper limb bone organ
proximal segment of free upper limb middle limb segment bone
proximal segment of free upper limb middle limb segment bone organ
proximal segment of free upper limb zeugopod bone
proximal segment of free upper limb zeugopod bone organ
zeugopod of proximal segment of free upper limb bone
zeugopod of proximal segment of free upper limb bone organ
A small sesamoid bone situated behind a condyle of the femur.
The ureteral branches of renal artery are small branches which supply the ureter.
An artery that is part of a respiratory system [Automatically generated definition].
The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose.
ramus labialis superior arteriae facialis
The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
ramus labialis inferior (arteria facialis)
ramus labialis inferior arteriae facialis
An artery that supplies blood to the cerebellum.
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
One of the arteries supplying a meninix[Automatically generated definition].
A vein that is part of a ureter [Automatically generated definition].
A vein that is part of a respiratory system [Automatically generated definition].
The inferior labial vein is the vein receiving blood from the upper lip.
The inferior labial vein is the vein receiving blood from the lower lip.
A vein that is part of a thoracic cavity [Automatically generated definition].
A vein that is part of a clitoris [Automatically generated definition].
A vein that is part of a tail [Automatically generated definition].
A portion of vein that is part of a trabecular bone tissue [Automatically generated definition].
A portion of lymphoid tissue that is part of a thymus [Automatically generated definition].
A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland.
A sebaceous gland that is part of a vagina [Automatically generated definition].
this class was obsoleted as it was defined inconsistently
A holocrine gland of the dermis that secretes sebum into hair follicles.
A lactiferous gland that is part of the abdominal region [Automatically generated definition].
Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
respiratory system capillary endothelium
A reticular lamina that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius fibroreticular lamina
apparatus respiratorius lamina fibroreticularis
apparatus respiratorius reticular lamina
fibroreticular lamina of apparatus respiratorius
fibroreticular lamina of respiratory system
lamina fibroreticularis of apparatus respiratorius
lamina fibroreticularis of respiratory system
respiratory system fibroreticular lamina
respiratory system lamina fibroreticularis
reticular lamina of apparatus respiratorius
A reticular lamina that is part of a bronchus [Automatically generated definition].
fibroreticular lamina of bronchial trunk
lamina fibroreticularis of bronchial trunk
A reticular lamina that is part of a trachea [Automatically generated definition].
fibroreticular lamina of cartilaginous trachea
lamina fibroreticularis of cartilaginous trachea
reticular lamina of cartilaginous trachea
A venule that is part of a respiratory system [Automatically generated definition].
An arteriole that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a head [Automatically generated definition].
A blood vessel that is part of an abdomen [Automatically generated definition].
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of a brain [Automatically generated definition].
A blood vessel that is part of a cornea [Automatically generated definition].
A blood vessel that is part of a retina [Automatically generated definition].
blood vessel of tunica interna of eyeball
A blood vessel that is part of a neck [Automatically generated definition].
A blood vessel that is part of a leg [Automatically generated definition].
A blood vessel that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a trachea.
A blood vessel that is part of a chest [Automatically generated definition].
anterolateral part of thorax blood vessel
blood vessel of anterior thoracic region
blood vessel of anterolateral part of thorax
A blood vessel that is part of an arm [Automatically generated definition].
blood vessel of proximal segment of free upper limb
proximal segment of free upper limb blood vessel
A blood vessel that is part of a toe [Automatically generated definition].
blood vessel of digit of terminal segment of free lower limb
blood vessel of terminal segment of free lower limb digit
digit of terminal segment of free lower limb blood vessel
terminal segment of free lower limb digit blood vessel
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a eyelid [Automatically generated definition].
A blood vessel that is part of a iris [Automatically generated definition].
A blood vessel that is part of a lung [Automatically generated definition].
A blood vessel that is part of a trunk [Automatically generated definition].
A blood vessel that is part of a limb [Automatically generated definition].
A blood vessel that is part of a forelimb [Automatically generated definition].
A blood vessel that is part of a hindlimb [Automatically generated definition].
A blood vessel that is part of a kidney [Automatically generated definition].
A blood vessel that is part of a main bronchus [Automatically generated definition].
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
A blood vessel that is part of a pelvis [Automatically generated definition].
A blood vessel that is part of a foot [Automatically generated definition].
blood vessel of autopod of inferior member
blood vessel of autopod of lower extremity
blood vessel of distal free limb segment of hind limb
blood vessel of distal free limb segment of hindlimb
blood vessel of distal free limb segment of inferior member
blood vessel of distal free limb segment of lower extremity
blood vessel of hind limb distal free limb segment
blood vessel of hindlimb distal free limb segment
blood vessel of inferior member distal free limb segment
blood vessel of lower extremity distal free limb segment
blood vessel of terminal segment of free lower limb
distal free limb segment of hind limb blood vessel
distal free limb segment of hindlimb blood vessel
distal free limb segment of inferior member blood vessel
distal free limb segment of lower extremity blood vessel
hind limb distal free limb segment blood vessel
hindlimb distal free limb segment blood vessel
inferior member distal free limb segment blood vessel
lower extremity distal free limb segment blood vessel
terminal segment of free lower limb blood vessel
A blood vessel that is part of a finger [Automatically generated definition].
blood vessel of digit of terminal segment of free upper limb
blood vessel of terminal segment of free upper limb digit
digit of terminal segment of free upper limb blood vessel
terminal segment of free upper limb digit blood vessel
A blood vessel that is part of a manus [Automatically generated definition].
arm distal free limb segment blood vessel
autopod of proximal segment of free upper limb blood vessel
blood vessel of arm distal free limb segment
blood vessel of autopod of brachial region
blood vessel of autopod of proximal segment of free upper limb
blood vessel of brachial region distal free limb segment
blood vessel of distal free limb segment of arm
blood vessel of distal free limb segment of brachial region
blood vessel of distal free limb segment of proximal segment of free upper limb
blood vessel of proximal segment of free upper limb autopod
blood vessel of proximal segment of free upper limb distal free limb segment
blood vessel of terminal segment of free upper limb
brachial region distal free limb segment blood vessel
distal free limb segment of arm blood vessel
distal free limb segment of brachial region blood vessel
distal free limb segment of proximal segment of free upper limb blood vessel
proximal segment of free upper limb autopod blood vessel
proximal segment of free upper limb distal free limb segment blood vessel
terminal segment of free upper limb blood vessel
A blood vessel that is part of a tail [Automatically generated definition].
A capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
capillary vessel of apparatus respiratorius
A capillary that is part of a kidney [Automatically generated definition].
A gray matter that is part of a brain [Automatically generated definition].
An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of lymph vessel
apparatus respiratorius lymph vessel endothelium
apparatus respiratorius lymphatic vessel endothelium
endothelium of lymph vessel of apparatus respiratorius
endothelium of lymph vessel of respiratory system
lymph vessel endothelium of apparatus respiratorius
lymph vessel endothelium of respiratory system
lymphatic vessel endothelium of apparatus respiratorius
lymphatic vessel endothelium of respiratory system
respiratory system endothelium of lymph vessel
respiratory system lymph vessel endothelium
respiratory system lymphatic vessel endothelium
A zone of skin that is part of a toe [Automatically generated definition].
digit of terminal segment of free lower limb skin
skin of digit of terminal segment of free lower limb
skin of terminal segment of free lower limb digit
terminal segment of free lower limb digit skin
A zone of skin that is part of a forelimb [Automatically generated definition].
TODO - check free limb vs pectoral complex
A zone of skin that is part of a hindlimb [Automatically generated definition].
TODO - check free limb vs pelvic complex
A zone of skin that is part of a finger [Automatically generated definition].
digit of terminal segment of free upper limb skin
skin of digit of terminal segment of free upper limb
skin of terminal segment of free upper limb digit
terminal segment of free upper limb digit skin
A zone of skin that is part of a tail [Automatically generated definition].
A nerve trunk that is part of a vagus nerve.
An alveolar duct that is part of a right lung [Automatically generated definition].
An alveolar duct that is part of a left lung [Automatically generated definition].
A bronchiole that is part of a right lung [Automatically generated definition].
A bronchiole that is part of a left lung [Automatically generated definition].
A terminal bronchiole that is part of a right lung [Automatically generated definition].
A terminal bronchiole that is part of a left lung [Automatically generated definition].
A respiratory bronchiole that is part of a right lung [Automatically generated definition].
A respiratory bronchiole that is part of a left lung [Automatically generated definition].
The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.
obsoleted as definition is unclear. cerebellar peduncle originally classified here but in ABA brainstem and cerbellum are spatially disjoint
A macula densa that is part of a distal convoluted tubule [Automatically generated definition].
A meninx that is part of a brain [Automatically generated definition].
Meninges that are part of the brain. [Bgee_curator][VHOG]
A meninx that is part of a forebrain [Automatically generated definition].
The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule.
The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]
A pia mater that is part of a forebrain [Automatically generated definition].
A pia mater that is part of a midbrain [Automatically generated definition].
Pia mater that is part of the midbrain. [Bgee_curator][VHOG]
A pia mater that is part of a telencephalon [Automatically generated definition].
Pia mater that is part of the telencephalon. [Bgee_curator][VHOG]
A pia mater that is part of a diencephalon [Automatically generated definition].
Pia mater that is part of the diencephalon. [Bgee_curator][VHOG]
mature diencephalon pia mater of neuraxis
pia mater of neuraxis of mature diencephalon
A pia mater that is part of a hindbrain [Automatically generated definition].
Pia mater that is part of the hindbrain. [Bgee_curator][VHOG]
A pia mater that is part of a spinal cord [Automatically generated definition].
An arachnoid mater that is part of a forebrain [Automatically generated definition].
arachnoid mater of neuraxis of forebrain
An arachnoid mater that is part of a midbrain [Automatically generated definition].
Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG]
An arachnoid mater that is part of a diencephalon [Automatically generated definition].
Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG]
arachnoid mater of neuraxis of between brain
arachnoid mater of neuraxis of diencephalon
arachnoid mater of neuraxis of interbrain
arachnoid mater of neuraxis of mature diencephalon
between brain arachnoid mater of neuraxis
diencephalon arachnoid mater of neuraxis
mature diencephalon arachnoid mater of neuraxis
An arachnoid mater that is part of a hindbrain [Automatically generated definition].
Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG]
arachnoid mater of neuraxis of hindbrain
An arachnoid mater that is part of a spinal cord [Automatically generated definition].
The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]
arachnoid mater of neuraxis of spinal cord
A dura mater that is part of a forebrain.
A dura mater that is part of a midbrain [Automatically generated definition].
Dura mater that is part of the midbrain. [Bgee_curator][VHOG]
A dura mater that is part of a telencephalon [Automatically generated definition].
A dura mater that is part of a diencephalon [Automatically generated definition].
Dura mater that is part of the diencephalon. [Bgee_curator][VHOG]
dura mater of neuraxis of mature diencephalon
mature diencephalon dura mater of neuraxis
A dura mater that is part of a hindbrain [Automatically generated definition].
Dura mater that is part of the hindbrain. [Bgee_curator][VHOG]
A portion of connective tissue that is part of a head [Automatically generated definition].
portion of connective tissue of adult head
A portion of connective tissue that is part of an abdomen [Automatically generated definition].
A portion of connective tissue that is part of a neck [Automatically generated definition].
neck (volume) portion of connective tissue
portion of connective tissue of neck (volume)
A portion of connective tissue that is part of a leg [Automatically generated definition].
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
A connective tissue that is part of a trachea.
portion of connective tissue of windpipe
A portion of connective tissue that is part of a chest [Automatically generated definition].
anterior thoracic region connective tissue
anterior thoracic region portion of connective tissue
anterior thoracic region textus connectivus
anterolateral part of thorax connective tissue
anterolateral part of thorax portion of connective tissue
anterolateral part of thorax textus connectivus
connective tissue of anterior thoracic region
connective tissue of anterolateral part of thorax
front of thorax portion of connective tissue
portion of connective tissue of anterior thoracic region
portion of connective tissue of anterolateral part of thorax
portion of connective tissue of front of thorax
textus connectivus of anterior thoracic region
textus connectivus of anterolateral part of thorax
A portion of connective tissue that is part of an arm [Automatically generated definition].
brachial region portion of connective tissue
connective tissue of proximal segment of free upper limb
portion of connective tissue of brachial region
portion of connective tissue of proximal segment of free upper limb
proximal segment of free upper limb connective tissue
proximal segment of free upper limb portion of connective tissue
proximal segment of free upper limb textus connectivus
textus connectivus of proximal segment of free upper limb
A portion of connective tissue that is part of a elbow [Automatically generated definition].
cubital region portion of connective tissue
portion of connective tissue of cubital region
A portion of connective tissue that is part of a wrist [Automatically generated definition].
carpal region portion of connective tissue
portion of connective tissue of carpal region
A portion of connective tissue that is part of a hip [Automatically generated definition].
portion of connective tissue of hip region
portion of connective tissue of regio coxae
regio coxae portion of connective tissue
A portion of connective tissue that is part of a knee [Automatically generated definition].
A portion of connective tissue that is part of a toe [Automatically generated definition].
connective tissue of digit of terminal segment of free lower limb
connective tissue of terminal segment of free lower limb digit
digit of foot portion of connective tissue
digit of terminal segment of free lower limb connective tissue
digit of terminal segment of free lower limb portion of connective tissue
digit of terminal segment of free lower limb textus connectivus
digitus pedis portion of connective tissue
portion of connective tissue of digit of foot
portion of connective tissue of digit of terminal segment of free lower limb
portion of connective tissue of digitus pedis
portion of connective tissue of foot digit
portion of connective tissue of terminal segment of free lower limb digit
terminal segment of free lower limb digit connective tissue
terminal segment of free lower limb digit portion of connective tissue
terminal segment of free lower limb digit textus connectivus
textus connectivus of digit of terminal segment of free lower limb
textus connectivus of terminal segment of free lower limb digit
A portion of connective tissue that is part of a shoulder [Automatically generated definition].
portion of connective tissue of shoulder
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
connective tissue of lower respiratory tract
lower respiratory tract portion of connective tissue
lower respiratory tract textus connectivus
portion of connective tissue of lower respiratory tract
textus connectivus of lower respiratory tract
lower respiratory tract connective tissue
A portion of connective tissue that is part of a eyelid [Automatically generated definition].
portion of connective tissue of blepharon
A portion of connective tissue that is part of a nasopharynx [Automatically generated definition].
connective tissue of nasal part of pharynx
nasal part of pharynx portion of connective tissue
nasal part of pharynx textus connectivus
nasopharynx portion of connective tissue
portion of connective tissue of nasal part of pharynx
portion of connective tissue of nasopharynx
portion of connective tissue of rhinopharynx
rhinopharynx portion of connective tissue
textus connectivus of nasal part of pharynx
A portion of connective tissue that is part of a larynx [Automatically generated definition].
The fibrous supportive tissue of the mammary gland.
connective tissue of lobe of mammary gland
lactiferous gland portion of connective tissue
lobe of breast portion of connective tissue
lobe of mammary gland portion of connective tissue
lobe of mammary gland textus connectivus
mammary gland portion of connective tissue
portion of connective tissue of lactiferous gland
portion of connective tissue of lobe of breast
portion of connective tissue of lobe of mammary gland
portion of connective tissue of mammary gland
textus connectivus of lobe of mammary gland
A portion of connective tissue that is part of a dermis [Automatically generated definition].
A portion of connective tissue that is part of a trunk [Automatically generated definition].
A portion of connective tissue that is part of a limb [Automatically generated definition].
A portion of connective tissue that is part of a forelimb [Automatically generated definition].
anteriormost limb portion of connective tissue
portion of connective tissue of anteriormost limb
portion of connective tissue of fore limb
portion of connective tissue of forelimb
portion of connective tissue of superior member
portion of connective tissue of upper extremity
superior member portion of connective tissue
upper extremity portion of connective tissue
A portion of connective tissue that is part of a hindlimb [Automatically generated definition].
inferior member portion of connective tissue
lower extremity portion of connective tissue
portion of connective tissue of hind limb
portion of connective tissue of hindlimb
portion of connective tissue of inferior member
portion of connective tissue of lower extremity
A portion of connective tissue that is part of a main bronchus [Automatically generated definition].
bronchus principalis portion of connective tissue
connective tissue of bronchus principalis
main bronchus portion of connective tissue
portion of connective tissue of bronchus principalis
portion of connective tissue of main bronchus
portion of connective tissue of primary bronchus
portion of connective tissue of principal bronchus
primary bronchus portion of connective tissue
principal bronchus portion of connective tissue
textus connectivus of bronchus principalis
textus connectivus of principal bronchus
A portion of connective tissue that is part of a lobar bronchus [Automatically generated definition].
lobar bronchus portion of connective tissue
portion of connective tissue of lobar bronchus
portion of connective tissue of secondary bronchus
secondary bronchus portion of connective tissue
textus connectivus of secondary bronchus
A portion of connective tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk portion of connective tissue
portion of connective tissue of bronchial trunk
portion of connective tissue of bronchus
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
cavity of chest portion of connective tissue
cavity of thorax portion of connective tissue
chest cavity portion of connective tissue
pectoral cavity portion of connective tissue
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
thoracic cavity portion of connective tissue
A portion of connective tissue that is part of a pelvis [Automatically generated definition].
A portion of connective tissue that is part of a foot [Automatically generated definition].
autopod of hind limb portion of connective tissue
autopod of hindlimb portion of connective tissue
autopod of inferior member connective tissue
autopod of inferior member portion of connective tissue
autopod of inferior member textus connectivus
autopod of lower extremity connective tissue
autopod of lower extremity portion of connective tissue
autopod of lower extremity textus connectivus
connective tissue of autopod of hind limb
connective tissue of autopod of hindlimb
connective tissue of autopod of inferior member
connective tissue of autopod of lower extremity
connective tissue of distal free limb segment of hind limb
connective tissue of distal free limb segment of hindlimb
connective tissue of distal free limb segment of inferior member
connective tissue of distal free limb segment of lower extremity
connective tissue of hind limb distal free limb segment
connective tissue of hindlimb distal free limb segment
connective tissue of inferior member autopod
connective tissue of inferior member distal free limb segment
connective tissue of lower extremity autopod
connective tissue of lower extremity distal free limb segment
connective tissue of terminal segment of free lower limb
distal free limb segment of hind limb connective tissue
distal free limb segment of hind limb portion of connective tissue
distal free limb segment of hind limb textus connectivus
distal free limb segment of hindlimb connective tissue
distal free limb segment of hindlimb portion of connective tissue
distal free limb segment of hindlimb textus connectivus
distal free limb segment of inferior member connective tissue
distal free limb segment of inferior member portion of connective tissue
distal free limb segment of inferior member textus connectivus
distal free limb segment of lower extremity connective tissue
distal free limb segment of lower extremity portion of connective tissue
distal free limb segment of lower extremity textus connectivus
hind limb autopod portion of connective tissue
hind limb distal free limb segment connective tissue
hind limb distal free limb segment portion of connective tissue
hind limb distal free limb segment textus connectivus
hindlimb autopod portion of connective tissue
hindlimb distal free limb segment connective tissue
hindlimb distal free limb segment portion of connective tissue
hindlimb distal free limb segment textus connectivus
inferior member autopod connective tissue
inferior member autopod portion of connective tissue
inferior member autopod textus connectivus
inferior member distal free limb segment connective tissue
inferior member distal free limb segment portion of connective tissue
inferior member distal free limb segment textus connectivus
lower extremity autopod connective tissue
lower extremity autopod portion of connective tissue
lower extremity autopod textus connectivus
lower extremity distal free limb segment connective tissue
lower extremity distal free limb segment portion of connective tissue
lower extremity distal free limb segment textus connectivus
portion of connective tissue of autopod of hind limb
portion of connective tissue of autopod of hindlimb
portion of connective tissue of autopod of inferior member
portion of connective tissue of autopod of lower extremity
portion of connective tissue of distal free limb segment of hind limb
portion of connective tissue of distal free limb segment of hindlimb
portion of connective tissue of distal free limb segment of inferior member
portion of connective tissue of distal free limb segment of lower extremity
portion of connective tissue of hind limb autopod
portion of connective tissue of hind limb distal free limb segment
portion of connective tissue of hindlimb autopod
portion of connective tissue of hindlimb distal free limb segment
portion of connective tissue of inferior member autopod
portion of connective tissue of inferior member distal free limb segment
portion of connective tissue of lower extremity autopod
portion of connective tissue of lower extremity distal free limb segment
portion of connective tissue of terminal segment of free lower limb
terminal segment of free lower limb connective tissue
terminal segment of free lower limb portion of connective tissue
terminal segment of free lower limb textus connectivus
textus connectivus of autopod of hind limb
textus connectivus of autopod of hindlimb
textus connectivus of autopod of inferior member
textus connectivus of autopod of lower extremity
textus connectivus of distal free limb segment of hind limb
textus connectivus of distal free limb segment of hindlimb
textus connectivus of distal free limb segment of inferior member
textus connectivus of distal free limb segment of lower extremity
textus connectivus of hind limb distal free limb segment
textus connectivus of hindlimb distal free limb segment
textus connectivus of inferior member autopod
textus connectivus of inferior member distal free limb segment
textus connectivus of lower extremity autopod
textus connectivus of lower extremity distal free limb segment
textus connectivus of terminal segment of free lower limb
A portion of connective tissue that is part of an ankle [Automatically generated definition].
A portion of connective tissue that is part of a finger [Automatically generated definition].
connective tissue of digit of terminal segment of free upper limb
connective tissue of terminal segment of free upper limb digit
digit of hand portion of connective tissue
digit of terminal segment of free upper limb connective tissue
digit of terminal segment of free upper limb portion of connective tissue
digit of terminal segment of free upper limb textus connectivus
digitus manus portion of connective tissue
portion of connective tissue of digit of hand
portion of connective tissue of digit of terminal segment of free upper limb
portion of connective tissue of digitus manus
portion of connective tissue of hand digit
portion of connective tissue of terminal segment of free upper limb digit
terminal segment of free upper limb digit connective tissue
terminal segment of free upper limb digit portion of connective tissue
terminal segment of free upper limb digit textus connectivus
textus connectivus of digit of terminal segment of free upper limb
textus connectivus of terminal segment of free upper limb digit
A portion of connective tissue that is part of a hand [Automatically generated definition].
arm autopod portion of connective tissue
arm distal free limb segment connective tissue
arm distal free limb segment portion of connective tissue
arm distal free limb segment textus connectivus
autopod of arm portion of connective tissue
autopod of brachial region connective tissue
autopod of brachial region portion of connective tissue
autopod of brachial region textus connectivus
autopod of proximal segment of free upper limb connective tissue
autopod of proximal segment of free upper limb portion of connective tissue
autopod of proximal segment of free upper limb textus connectivus
brachial region autopod connective tissue
brachial region autopod portion of connective tissue
brachial region autopod textus connectivus
brachial region distal free limb segment connective tissue
brachial region distal free limb segment portion of connective tissue
brachial region distal free limb segment textus connectivus
connective tissue of arm distal free limb segment
connective tissue of autopod of brachial region
connective tissue of autopod of proximal segment of free upper limb
connective tissue of brachial region autopod
connective tissue of brachial region distal free limb segment
connective tissue of distal free limb segment of arm
connective tissue of distal free limb segment of brachial region
connective tissue of distal free limb segment of proximal segment of free upper limb
connective tissue of proximal segment of free upper limb autopod
connective tissue of proximal segment of free upper limb distal free limb segment
connective tissue of terminal segment of free upper limb
distal free limb segment of arm connective tissue
distal free limb segment of arm portion of connective tissue
distal free limb segment of arm textus connectivus
distal free limb segment of brachial region connective tissue
distal free limb segment of brachial region portion of connective tissue
distal free limb segment of brachial region textus connectivus
distal free limb segment of proximal segment of free upper limb connective tissue
distal free limb segment of proximal segment of free upper limb portion of connective tissue
distal free limb segment of proximal segment of free upper limb textus connectivus
portion of connective tissue of arm autopod
portion of connective tissue of arm distal free limb segment
portion of connective tissue of autopod of arm
portion of connective tissue of autopod of brachial region
portion of connective tissue of autopod of proximal segment of free upper limb
portion of connective tissue of brachial region autopod
portion of connective tissue of brachial region distal free limb segment
portion of connective tissue of distal free limb segment of arm
portion of connective tissue of distal free limb segment of brachial region
portion of connective tissue of distal free limb segment of proximal segment of free upper limb
portion of connective tissue of proximal segment of free upper limb autopod
portion of connective tissue of proximal segment of free upper limb distal free limb segment
portion of connective tissue of terminal segment of free upper limb
proximal segment of free upper limb autopod connective tissue
proximal segment of free upper limb autopod portion of connective tissue
proximal segment of free upper limb autopod textus connectivus
proximal segment of free upper limb distal free limb segment connective tissue
proximal segment of free upper limb distal free limb segment portion of connective tissue
proximal segment of free upper limb distal free limb segment textus connectivus
terminal segment of free upper limb connective tissue
terminal segment of free upper limb portion of connective tissue
terminal segment of free upper limb textus connectivus
textus connectivus of arm distal free limb segment
textus connectivus of autopod of brachial region
textus connectivus of autopod of proximal segment of free upper limb
textus connectivus of brachial region autopod
textus connectivus of brachial region distal free limb segment
textus connectivus of distal free limb segment of arm
textus connectivus of distal free limb segment of brachial region
textus connectivus of distal free limb segment of proximal segment of free upper limb
textus connectivus of proximal segment of free upper limb autopod
textus connectivus of proximal segment of free upper limb distal free limb segment
textus connectivus of terminal segment of free upper limb
A portion of connective tissue that is part of a tail [Automatically generated definition].
portion of connective tissue of post-vent region
post-vent region portion of connective tissue
A cartilage that is part of a neck [Automatically generated definition].
A cartilage that is part of a lower respiratory tract [Automatically generated definition].
the ring-shaped cartilaginous structures that support the trachea
check whether to classify as part of splanchoncranium
in mammals the rings are incomplete, in avians the rings are complete.
A skin gland that is part of a camera-type eye [Automatically generated definition].
A long bone that is part of a limb [Automatically generated definition].
A long bone that is part of a forelimb [Automatically generated definition].
A long bone that is part of a hindlimb [Automatically generated definition].
The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall.
adult aorta textus connectivus elasticus
dorsal aorta textus connectivus elasticus
elastic connective tissue of adult aorta
elastic connective tissue of dorsal aorta
elastic connective tissue of trunk of aortic tree
textus connectivus elasticus of adult aorta
textus connectivus elasticus of dorsal aorta
textus connectivus elasticus of trunk of aortic tree
trunk of aortic tree elastic connective tissue
trunk of aortic tree textus connectivus elasticus
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
An elastic tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius elastic connective tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
An elastic tissue that is part of a circulatory system [Automatically generated definition].
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
A tissue that is found in the tunica media of the vessels wall and allows vessels to stretch.
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
textus connectivus elasticus of blood vessel
Elastic tissue that is part of a lung [Automatically generated definition].
An elastic tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk elastic connective tissue
bronchial trunk textus connectivus elasticus
elastic connective tissue of bronchial trunk
textus connectivus elasticus of bronchial trunk
textus connectivus elasticus of bronchus
An elastic tissue that is part of a trachea [Automatically generated definition].
cartilaginous trachea elastic connective tissue
cartilaginous trachea textus connectivus elasticus
elastic connective tissue of cartilaginous trachea
elastic connective tissue of vertebrate trachea
textus connectivus elasticus of cartilaginous trachea
textus connectivus elasticus of vertebrate trachea
textus connectivus elasticus of windpipe
vertebrate trachea elastic connective tissue
vertebrate trachea textus connectivus elasticus
The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers.
The innermost layer of the aorta, containing the endothelium and an inner elastic membrane.
A phalanx that is part of a hand digit 1 [Automatically generated definition].
Pollex ; Digitus primus [ I ] digit long bone
Pollex ; Digitus primus [ I ] long bone of digit
digit long bone of Pollex ; Digitus primus [ I ]
long bone of digit of Pollex ; Digitus primus [ I ]
long bone of digit of first digit of hand
phalanx of Pollex ; Digitus primus [ I ]
Anurans lack manual digit 1, so manual digit 2 is the digit after the prepollex (Phenotype RCN Oct 2012)
A phalanx that is part of a hand digit 2 [Automatically generated definition].
long bone of digit of 2 nd digit of hand
A phalanx that is part of a hand digit 3 [Automatically generated definition].
long bone of digit of 3 rd digit of hand
A phalanx that is part of a hand digit 4 [Automatically generated definition].
long bone of digit of 4 th digit of hand
A phalanx that is part of a hand digit 5 [Automatically generated definition].
long bone of digit of 5 th digit of hand
A phalanx that is part of a foot digit 1 [Automatically generated definition].
A phalanx that is part of a foot digit 2 [Automatically generated definition].
A phalanx that is part of a foot digit 3 [Automatically generated definition].
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
An arterial blood vessel that is part of a kidney [Automatically generated definition].
A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 1.
The first metacarpal bone or the metacarpal bone of the thumb is the first bone of the thumb. It is connected to the trapezium of the carpus at the first carpometacarpal joint and to the proximal thumb phalanx at the first metacarpophalangeal joint[Wikipedia:First_metacarpal_bone].
metacarpal bone of Pollex ; Digitus primus [ I ]
metacarpal of Pollex ; Digitus primus [ I ]
pollex ; digitus primus [ I ] metacarpal
pollex ; digitus primus [ I ] metacarpal bone
A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 2.
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and carpal 2(1) or carpal 2+3(1+2) proximally and with the proximal phalanx of digit II(I) distally.[AAO]
A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 3[Automatically generated definition].
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with carpal 3(2) proximally and with the proximal phalanx of digit III(II) distally.[AAO]
The third metacarpal bone (metacarpal bone of the middle finger) is a little smaller than the second. The dorsal aspect of its base presents on its radial side a pyramidal eminence, the styloid process, which extends upward behind the capitate; immediately distal to this is a rough surface for the attachment of the extensor carpi radialis brevis muscle. The carpal articular facet is concave behind, flat in front, and articulates with the capitate. On the radial side is a smooth, concave facet for articulation with the second metacarpal, and on the ulnar side two small oval facets for the fourth metacarpal[Wikipedia:Third_metacarpal_bone].
A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 4.
The fourth metacarpal bone (metacarpal bone of the ring finger) is shorter and smaller than the third. The base is small and quadrilateral; its superior surface presents two facets, a large one medially for articulation with the hamate, and a small one laterally for the capitate. On the radial side are two oval facets, for articulation with the third metacarpal; and on the ulnar side a single concave facet, for the fifth metacarpal[Wikipedia:Fourth_metacarpal_bone].
A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 5.
Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that articulates with carpal 5(4) proximally and with the proximal phalanx of digit V(IV) distally.[AAO]
The fifth metacarpal bone (metacarpal bone of the little finger or pinky finger) is the most lateral metacarpal[Wikipedia:Fifth_metacarpal_bone].
FMA also has FMA:36782 ! Bone of fifth metacarpal bone
A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 1.
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and tarsal 1 proximally and with the proximal phalanx of digit I distally.[AAO]
The first metatarsal bone is the bone in the body of the foot just behind the big toe. It is remarkable for its great thickness, and is the shortest of the metatarsal bones. The body is strong, and of well-marked prismoid form. The base presents, as a rule, no articular facets on its sides, but occasionally on the lateral side there is an oval facet, by which it articulates with the second metatarsal. Its proximal articular surface is of large size and kidney-shaped; its circumference is grooved, for the tarsometatarsal ligaments, and medially gives insertion to part of the tendon of the Tibialis anterior; its plantar angle presents a rough oval prominence for the insertion of the tendon of the Peronæus longus. The head is large; on its plantar surface are two grooved facets, on which glide sesamoid bones; the facets are separated by a smooth elevation[Wikipedia:First_metatarsal_bone].
A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 2.
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 2 proximally and with the proximal phalanx of digit II distally.[AAO]
A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 3[Automatically generated definition].
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 3 proximally and with the proximal phalanx of digit III distally.[AAO]
The third metatarsal bone articulates proximally, by means of a triangular smooth surface, with the third cuneiform; medially, by two facets, with the second metatarsal; and laterally, by a single facet, with the fourth metatarsal. This last facet is situated at the dorsal angle of the base[Wikipedia:Third_metatarsal_bone].
A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 4.
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 4 or the distal head of the tibiale-fibulare proximally and with the proximal phalanx of digit IV distally.[AAO]
The fourth metatarsal bone is smaller in size than the third; its base presents an oblique quadrilateral surface for articulation with the cuboid; a smooth facet on the medial side, divided by a ridge into an anterior portion for articulation with the third metatarsal, and a posterior portion for articulation with the third cuneiform; on the lateral side a single facet, for articulation with the fifth metatarsal[Wikipedia:Fourth_metatarsal_bone].
A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 5.
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 5 or the distal head of the tibiale-fibulare proximally and with the proximal phalanx of digit V distally.[AAO]
The fifth metatarsal bone is recognized by a rough eminence, the tuberosity, on the lateral side of its base. The base articulates behind, by a triangular surface cut obliquely in a transverse direction, with the cuboid; and medially, with the fourth metatarsal. On the medial part of its dorsal surface is inserted the tendon of the Peronæus tertius and on the dorsal surface of the tuberosity that of the Peronæus brevis. A strong band of the plantar aponeurosis connects the projecting part of the tuberosity with the lateral process of the tuberosity of the calcaneus. The plantar surface of the base is grooved for the tendon of the Abductor digiti quinti, and gives origin to the Flexor digiti quinti brevis. The base of the metatarsal is often injured and a particularly notorious fracture is the Jones fracture. When the tuberosity is broken, it is called a pseudo-Jones fracture or a dancer's fracture. This is a common fracture of the fifth metatarsal. Stress fractures are common in the fifth metatarsal among athletes[Wikipedia:Fifth_metatarsal_bone].
Molars are the rearmost and most complicated kind of tooth in most mammals.
Human variation notes: Adult humans have twelve molars, in four groups of three at the back of the mouth. The third, rearmost molar in each group is called a wisdom tooth. It is the last tooth to appear, breaking through the surface of the gum at about the age of twenty, although this varies from individual to individual. Ethnicity can also have an impact on the age at which this occurs, with statistical variations between groups. The human mouth contains upper (maxillary) and lower (mandibular) molars. They are: maxillary first molar, maxillary second molar, maxillary third molar, mandibular first molar, mandibular second molar, and mandibular third molar.
A bone that is part of a mesopodial skeleton.
The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost
Any joint that is part of a (free) limb.
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
A muscle organ that is part of a hip [Automatically generated definition].
A muscle organ that is part of a toe [Automatically generated definition].
digit of terminal segment of free lower limb muscle organ
muscle organ of digit of terminal segment of free lower limb
muscle organ of terminal segment of free lower limb digit
terminal segment of free lower limb digit muscle organ
The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle].
A muscle organ that is part of a limb [Automatically generated definition].
A muscle organ that is part of a forelimb.
FMA and MA class actually refer to muscles of entire pectoral complex
A muscle organ that is part of a hindlimb [Automatically generated definition].
A muscle organ that is part of a finger [Automatically generated definition].
digit of terminal segment of free upper limb muscle organ
muscle organ of digit of terminal segment of free upper limb
muscle organ of terminal segment of free upper limb digit
terminal segment of free upper limb digit muscle organ
A muscle organ that attaches to a tail vertebra [Automatically generated definition].
the BTO class may possibly refer to an invertebrate structure
A molar tooth that is part of a upper jaw [Automatically generated definition].
A molar tooth that is part of a lower jaw [Automatically generated definition].
A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body.
The deep fascia of the thigh. [WP,unvetted].
A combination of exfoliated (shed) epithelial cells, transudated skin oils, and moisture. It occurs in both female and male mammalian genitalia[WP].
A major stabilizing ligament in the knee that attaches the surfaces of the femur and tibia.
anterior cruciate ligament of knee joint
A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl.
Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO]
The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition])
A tooth that is typically long and pointed and bearing a single cusp.
Most species that develop them normally have four per individual, two in the upper jaw and two in the lower, separated within each jaw by its incisors; humans and dogs are examples. In most animals, canines are the anterior-most teeth in the maxillary bone. The four canines in humans are the two maxillary canines and the two mandibular canines.
The portion of the tooth covered by enamel.
The central portion of the common tendon of the quadriceps femoris. It is attached to the apex of the PATELLA and to the lower part of the tubercle of the TIBIA.
central band of tendon of quadriceps femoris
The ventral area of the mouth. In organisms with a tongue, this is the area under the ventral surface of the tongue[ncit, modified].
posterior cruciate ligament of knee joint
In humans: Muscles arising in the zygomatic arch that close the jaw. Their nerve supply is masseteric from the mandibular division of the trigeminal nerve. (From Stedman, 25th ed)
we use this specifically for a jaw muscle that is innervates by the mandibular nerve.
originate from the somitomeres. These muscles develop late and are not complete even at birth. Tongue muscles develop before masticatory muscles and complete by birth
The muscles of the palate are the glossopalatine, palatoglossus, levator palati(ni), musculus uvulae, palatopharyngeus, and tensor palati(ni).
see also FMA:71438 ! set of muscles of soft palate and fauces
A group of muscles and their tendons that act to stabilize the shoulder. The four muscles of the rotator cuff are over half of the seven scapulohumeral muscles
body cavity of the human body (and animal bodies) that holds the bulk of the viscera. It is located below (or inferior to) the thoracic cavity, and above the pelvic cavity. It is a part of the abdominopelvic cavity. Organs of the abdominal cavity include the stomach, liver, gallbladder, spleen, pancreas, small intestine, kidneys, and large intestine. The abdominal cavity is lined with a protective membrane termed the peritoneum. The kidneys are located in the abdominal cavity behind the peritoneum, in the retroperitoneum. The viscera are also covered, in the front, with a layer of peritoneum called the greater omentum (or omental apron).
Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture.
Dental alveolus (plural, alveoli) are sockets in the jaws in which the roots of teeth are held in the alveolar process of maxilla with the periodontal ligament. The lay term for dental alveoli is tooth sockets. A joint that connect the roots of the teeth and the alveolus are called gomphosis (plural gomphoses). In mammals, tooth sockets are found in the maxilla and the mandible. [WP,unvetted].
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
A fold of peritoneum originating at the stomach and supporting the viscera.
The sella turcica is a saddle-shaped depression in the sphenoid bone at the base of the human skull. [WP,unvetted].
for consistency with FMA we have a separate class for the cavity of the sella turcica
A collection of sacral vertebrae in the sacral region that are fused and part of the bony pelvis.
the AAO class 'sacrum' is deliberately placed under 'sacral vertebra' rather than here
The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater.
In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus
in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail
The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula.
Anatomical space in the abdominal cavity behind (retro) the peritoneum. It has no specific delineating anatomical structures. Organs are retroperitoneal if they only have peritoneum on their anterior side.
The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas.
The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted].
we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part
The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral.
we follow FMA in making these joints part of digits
The abdominal wall represents the boundaries of the abdominal cavity. The abdominal wall is split into the posterior (back), lateral (sides) and anterior (front) walls. There is a common set of layers covering and forming all the walls: the deepest being the extraperitoneal fat, the parietal peritoneum, and a layer of fascia which has different names over where it covers (eg transversalis, psoas fascia). Superficial to these, but not present in the posterior wall are the three layers of muscle, the transversus abdominis (transverse abdominal muscle), the internal (obliquus internus) and the external oblique (obliquus externus).
A joint of the pes that connects the talus and the calcaneus.
The firm fibrocartilaginous joint in the median plane between the two opposing surfaces of the pubic bones, which are united by an interpubic disc of fibrocartilage as well as the superior and arcuate pubic ligaments.
Medial attachment of the two halves of the pelvic girdle.[AAO]
In birds, the pubic symphysis is present only in the ostrich, and the two hip bones are usually widely separated, making it easier to lay large eggs - Romer, Alfred Sherwood; Parsons, Thomas S. (1977). The Vertebrate Body. Philadelphia, PA: Holt-Saunders International. pp. 188–192. ISBN 0-03-910284-X.
A joint of the jaw that connects the mandible to a temporal bone. There are two TMJs, one on either side, working in unison. The unique feature of the TMJs is the articular disc. The disc is composed of fibrocartilagenous tissue (like the firm and flexible elastic cartilage of the ear) which is positioned between the two bones that form the joint. The TMJs are one of the only synovial joints in the human body with an articular disc, another being the sternoclavicular joint. The disc divides each joint into two. The lower joint compartment formed by the mandible and the articular disc is involved in rotational movement -- this is the initial movement of the jaw when the mouth opens. The upper joint compartment formed by the articular disk and the temporal bone is involved in translational movement -- this is the secondary gliding motion of the jaw as it is opened widely. The part of the mandible which mates to the under-surface of the disc is the condyle and the part of the temporal bone which mates to the upper surface of the disk is the glenoid (or mandibular) fossa[WP].
The Achilles tendon is a tendon of the posterior leg. It serves to attach the plantaris, gastrocnemius (calf) and soleus muscles to the calcaneus (heel) bone.
in FMA this is a ligament, and part of the muscle
the passage in the lower abdominal wall through which the spermatic cord in the male or the round ligament in the female, nerves and vessels pass from the pelvic cavity to the scrotum or labia majora, respectively
In most mammals the canal remains open, and the testis can pass from the scrotum to the abdominal cavity. In humans the canal closes after testicular descent[doi:10.1046/j.1469-7580.2002.00087.x]
In tammar wallabies, closes between days 50 and 60 pp[doi:10.1046/j.1469-7580.2002.00087.x]
Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.
Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.
Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]
A small bulge in the small intestine present at birth. It is a vestigial remnant of the omphalomesenteric duct
Either of two pairs of folds of mucous membrane projecting into the larynx.
one of the anatomic dilations of the ascending aorta, which occurs just above the aortic valve.
In human anatomy, the carotid sinus is a localized dilation of the internal carotid artery at its origin, the common carotid artery bifurcation. A synonym for the carotid sinus is the carotid bulb. [WP,unvetted].
A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle
In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis
Nutrient blood vessels which supply the walls of large arteries or veins.
The aorta of swine contains a vaso vasorum like humans - http://www.nal.usda.gov/awic/pubs/swine/swine.htm#art
The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava.
The cavernous sinus (or lateral sellar compartment), within the human head, is a large collection of thin-walled veins creating a cavity bordered by the temporal bone of the skull and the sphenoid bone, lateral to the sella turcica.
An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334].
In anatomy, the splenic vein (in the past called the lienal vein) is the blood vessel that drains blood from the spleen. It joins with the superior mesenteric vein, to form the hepatic portal vein and follows a course superior to the pancreas, alongside of the similarly named artery, the splenic artery. It collects branches from the stomach and pancreas and most notably from the large intestine, which is drained by the inferior mesenteric vein and joins with splenic vein shortly before it forms the portal vein. [WP,unvetted].
Portion of tissue which consists of neurons, neuroglia and vasculature. Examples: Neural tissue of brain, neural tissue of peripheral ganglion, neural tissue of nerve[FMA].
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia.
A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch.
Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754].
recurrent laryngeal nerve from vagus nerve
vagus X nerve recurrent laryngeal branch
The sensory organs in muscle that are involved in the stretch reflex.
Any of the rapidly adapting mechanoreceptors found in subcutaneous tissue beneath both hairy and glabrous skin, and which normally contain an afferent nerve fiber surrounded by a capsule with multiple concentric layers.
The floor of the anterior fossa is formed by the orbital plates of the frontal, the cribriform plate of the ethmoid, and the small wings and front part of the body of the sphenoid; it is limited behind by the posterior borders of the small wings of the sphenoid and by the anterior margin of the chiasmatic groove. The lesser wings of the sphenoid separate the anterior and middle fossae.
The compartment containing the anterior extremities and half the inferior surface of the temporal lobes (TEMPORAL LOBE) of the cerebral hemispheres. Lying posterior and inferior to the anterior cranial fossa (CRANIAL FOSSA, ANTERIOR), it is formed by part of the TEMPORAL BONE and SPHENOID BONE. It is separated from the posterior cranial fossa (CRANIAL FOSSA, POSTERIOR) by crests formed by the superior borders of the petrous parts of the temporal bones[MESH]. The middle fossa, deeper than the anterior cranial fossa, is narrow medially and widens laterally to the sides of the skull. It is separated from the posterior fossa by the clivus and the petrous crest. It is bounded in front by the posterior margins of the lesser wings of the sphenoid bone, the anterior clinoid processes, and the ridge forming the anterior margin of the chiasmatic groove; behind, by the superior angles of the petrous portions of the temporal bones and the dorsum sellC&; laterally by the temporal squamC&, sphenoidal angles of the parietals, and greater wings of the sphenoid. It is traversed by the squamosal, sphenoparietal, sphenosquamosal, and sphenopetrosal sutures[WP].
The vestibular nerve is one of the two branches of the Vestibulocochlear nerve (the cochlear nerve being the other). It goes to the semicircular canals via the vestibular ganglion. It receives positional information. Axons of the vestibular nerve synapse in the vestibular nucleus on the lateral floor and wall of the fourth ventricle in the pons and medulla. It arises from bipolar cells in the vestibular ganglion, ganglion of Scarpa, which is situated in the upper part of the outer end of the internal auditory meatus. [WP,unvetted].
vestibulocochlear VIII nerve vestibular component
The musculocutaneous nerve arises from the lateral cord of the brachial plexus, opposite the lower border of the Pectoralis minor, its fibers being derived from C5, C6, C7. [WP,unvetted].
The cervical plexus is a plexus of the ventral rami of the first four cervical spinal nerves which are located from C1 to C5 cervical segment in the neck. They are located laterally to the transverse processes between prevertebral muscles from the medial side and vertebral from lateral side. Here there is anastomosis with accessory nerve, hypoglossal nerve and sympathetic trunk. It is located in the neck, deep to sternocleidomastoid. Nerves formed from the cervical plexus innervate the back of the head, as well as some neck muscles. The branches of the cervical plexus emerge from the posterior triangle at the nerve point, a point which lies midway on the posterior border of the Sternocleidomastoid[WP].
The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls.
The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted].
A central thoracic cavity surrounded by loose connective tissue that contains (where present) the heart, the great vessels of the heart, esophagus, trachea, phrenic nerve, cardiac nerve, thoracic duct, thymus, and lymph nodes of the central chest.
In humans, the mediastinum lies between the right and left pleura in and near the median sagittal plane of the chest. It extends from the sternum in front to the vertebral column behind, and contains all the thoracic viscera except the lungs. It may be divided for purposes of description into two parts:an upper portion, above the upper level of the pericardium, which is named the superior mediastinum with its superior limit at the superior thoracic opening and its inferior limit at the plane from the sternal angle to the disc of T4-T5 (Plane of Ludwig at Angle of Louis); and a lower portion, below the upper level of the pericardium. This lower portion is again subdivided into three parts, viz. that in front of the pericardium, the anterior mediastinum; that containing the pericardium and its contents, the middle mediastinum; and that behind the pericardium, the posterior mediastinum. It is surrounded by the chest wall anteriorly, the lungs laterally and the spine posteriorly. It is continuous with the loose connective tissue of the neck, and extends inferiorly onto the diaphragm
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
A region of the fetal urogenital sinus epithelium destined to become the prostate[GO].
AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204]
The part of the forelimb between pectoral region and the elbow, corresponding to the humerus.
Segment of the hindleg corresponding to the humerus.[AAO]
anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group.
The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants.
FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion
A nerve that is part of a thorax [Automatically generated definition].
A nerve that is part of an abdominal segment of trunk [Automatically generated definition].
A bone that is part of a hindlimb stylopod [Automatically generated definition].
May be merged into femur. See https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376
A bone that is part of a thorax [Automatically generated definition].
A bone that is part of an abdominal segment of trunk [Automatically generated definition].
bone organ of abdominal segment of trunk
A muscle structure that is part of a urethra [Automatically generated definition].
A muscle organ that is part of a thorax [Automatically generated definition].
A muscle organ that is part of a respiratory system [Automatically generated definition].
A muscle organ that is part of a esophagus [Automatically generated definition].
A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition].
muscle organ of abdominal segment of trunk
A blood vessel that is part of a thorax [Automatically generated definition].
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
blood vessel of abdominal segment of trunk
A skin of body that is part of an abdominal segment of trunk [Automatically generated definition].
A portion of connective tissue that is part of a thorax [Automatically generated definition].
A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition].
abdominal segment of trunk connective tissue
abdominal segment of trunk portion of connective tissue
abdominal segment of trunk textus connectivus
connective tissue of abdominal segment of trunk
portion of connective tissue of abdominal segment of trunk
textus connectivus of abdominal segment of trunk
A limb joint that is part of a forelimb [Automatically generated definition].
A limb joint that is part of a hindlimb [Automatically generated definition].
A limb joint that is part of an autopod [Automatically generated definition].
joint of limb of distal free limb segment
An anatomical space that surrounded_by a neural tube.
Epithelium that is part of a developing tooth or dental organ.
In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)
An epithelium that is part of a upper eyelid [Automatically generated definition].
An epithelium that is part of a lower eyelid [Automatically generated definition].
An epithelium that is part of a thymus, forming a supporting framework[MP,modified].
Part of the external carotid which supplies blood to the thyroid gland.[AAO]
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a telencephalon.
Cranial neural crest that is part of the telencephalon.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a diencephalon.
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
Mesenchyme that is part of a developing gonad [Automatically generated definition].
Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla.
we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme
Mesenchyme enclosed by dental organ.[MP]
Mesenchyme enclosed by dental organ.[TAO]
Mesenchyme that is part of a developing upper eyelid [Automatically generated definition].
Mesenchyme that is part of a developing lower eyelid [Automatically generated definition].
Mesenchyme that is part of a developing forelimb [Automatically generated definition].
Mesenchyme that is part of a developing hindlimb [Automatically generated definition].
posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine. .
A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO]
Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO]
the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process)
relationship loss: develops_from basidorsal (TAO:0001060)[TAO]
(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]
tiny neural arches present in Hagfish (which lack a true vertebraal column).
The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone
A phalanx that is part of a foot digit 4 [Automatically generated definition].
A phalanx that is part of a foot digit 5 [Automatically generated definition].
A middle phalanx that is part of a finger [Automatically generated definition].
A distal phalanx that is part of a finger [Automatically generated definition].
This is typically proximally connected to the middle phalanx of manus, except in some cases such as the human thumb, where it connects to the proximal phalanx. It always connects to some phalanx, by definition
A middle phalanx that is part of a toe [Automatically generated definition].
A distal phalanx that is part of a pedal digit [Automatically generated definition].
This is typically proximally connected to the middle phalanx of pes, except in some cases such as the human big toe, where it connects to the proximal phalanx. It always connects to some phalanx, by definition
A proximal phalanx that is part of a pedal digit [Automatically generated definition].
A presumptive structure that has_potential_to_develop_into a ganglion.
a part or parts of the hippocampus that have a particular function
Part of hippocampus proper bounded by CA2 and the subiculum, characterized by pyramidal neurons that receive projections from pyramidal neurons of CA3 via the Schaffer collaterals.
Part of hippocampus proper bounded by areas CA3 and CA1, characterized by a narrow layer of large pyramidal cells, similar in size to CA3 pyramidal cells, but which lack the mossy fiber input from the dentate gyrus (adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460)
Part of hippocampus proper bounded by the hilus of the dentate gyrus and area CA2, characterized by large pyramidal cells and a dense projection from dentate gyrus granule cell mossy fibers.
The last of four regions in the cornu ammonis of the hippocampus and is also part of the hilus of the dentate gyrus. This area contains mostly mossy cells that receive inputs from the dentate gyrus and pyramidal cells in the CA3 region and also projects back to the dentate gyrus.
consider obsoleting. consider - CA3c, hilus
A mesentery that is part of a uterus [Automatically generated definition].
An anatomical cavity that has_potential_to_develop_into a coelemic cavity lumen.
the part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
the fluid-filled spaces formed within the mass of extraembryonic mesoderm that later fuse to become a large extraembryonic cavity
Initial section of the oviduct through which the ova pass from the ovary to the uterus
paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]
Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]
In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]
Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct
Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.
A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP].
see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells
A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ
Portion of myotome that is ventral to the horizontal septum
A muscle organ that is part of a body wall [Automatically generated definition].
obsoleted as it grouped together a worm-specific structure (BTO) with the vertebrate structure (which develops from the myotome)
One of the skeletal muscles of the head and neck, spine, and ribs.
A portion of skeletal muscle tissue in the trunk.
Portion of myotome that is dorsal to the horizontal septum
A logitudinal sheet of continuous connective tissue partition developing at the apex of the chevron-shaped myotome and separating dorsal (epaxial) and ventral (hypaxial) body wall muscle masses; each is destined to become, respectively, the epaxial and hyopaxial musculature.
A connective tissue partition developing at the apex of the chevron-shaped myotome and separating dorsal (epaxial) and ventral (hypaxial) body wall muscle masses. Kimmel et al, 1995.[TAO]
relationship loss: subclass myoseptum (TAO:0001089)[TAO]
The part of the retina that contains neurons and photoreceptor cells[GO].
An epithelial and lymphoid organ that develops as a dorsal diverticulum of the proctodeal region of the cloaca in birds. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells[WP]. The bursa is an organ found in birds involved in B cell differentiation[GO].
Follicle containing part of bursa of Fabricius. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells[WP].
Follicle within the plicae of bursa of Fabricius.
Portion of extracellular matrix between the myocardium and the endocardium. The cardiac jelly plays a central role in the septation of the heart and comprises most of the thickness of the heart wall at early stages, but disappears as the heart differentiates.
The extracellular matrix between the myocardium and the endocardium. The cardiac jelly plays a central role in the septation of the heart and comprises most of the thickness of the heart wall at early stages, but disappears as the heart differentiates.[TAO]
An atrioventricular canal that is in the left side of a atrioventricular region.
An atrioventricular canal that is in the right side of a atrioventricular region.
small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP].
Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]
some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined).
endothelium of irregular blood filled space
wide vessels in the spleen that drain into trabecular veins[WP].
Whereas man and the rat are in the 'sinusal' group, the mouse belongs in the 'nonsinusal' group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml
An epithelium that is part of a choroid plexus [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue
chorioid plexus of cerebral hemisphere epithelium
epithelial tissue of chorioid plexus of cerebral hemisphere
epithelium of chorioid plexus of cerebral hemisphere
tooth-like structure composed of chitin.
hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
In EHDAA2, the developing spinal cord is classified as an epithelial tube
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
A mass of closely packed fat cells (adipose tissue) surrounded by fibrous tissue septa[TMD].
An accumulation of adipose tissue (fat cells) enclosed in fibrous tissue[BTO].
FMA says isa fascia organ. Note that XAO and AAO have structures called fat pad/body, but these are gonad-associated, so we place them with the gonad-specific subclass
An insect gland dorsal to the insect gut, with a function analogous to that of the vertebrate liver. It is a storage organ for fats, glycogen and protein and is a major site of intermediary metabolism.
A fatty tissue especially of nearly mature insect larvae that serves as a food reserve[BTO].
Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].
A blood vessel that carries blood from the capillaries toward the heart
embryonic structure that develops into pancreatic bud.
in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds
revisit after standardizing terms 'primordium', 'anlagen', 'bud'
The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID].
pancreatic bud that gives rise to the accessory pancreatic duct.
The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]
In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]
pancreatic bud that gives rise to the major pancreatic duct.
The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship.
Layer of the retina composed of the inner segments of the photoreceptor cells.
retina photoreceptor layer inner segment
retina photoreceptor layer outer segment
This term was obsoleted as it was previously defined midleadingly as 'A macula that is part of a cochlea'.
A duct that is part of a digestive system [Automatically generated definition].
An epithelium that is part of a digestive tract [Automatically generated definition].
Epithelium lining the lumen of the gut.[TAO]
epithelial tissue of lower gastrointestinal tract
epithelium of lower gastrointestinal tract
lower gastrointestinal tract epithelial tissue
Endocardium that is part of the atrioventricular canal[ZFA,vetted].
White matter that is part of a diencephalon [Automatically generated definition].
predominantly white regional part of diencephalon
A cartilage element of chondrocranium. Example: neurocranial trabecula.
A cartilage element that is part of the cranial skeleton.
Cartilage which is part of the cranium.[TAO]
Mesenchyme that is part of a developing pectoral fin [Automatically generated definition].
Mesenchyme that is part of the pectoral fin.[TAO]
Mesenchyme that is part of a developing pelvic fin [Automatically generated definition].
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
The area of the parietal lobe that integrates tactile and visual stimuli
The area of the temporal lobe concerned with hearing[MP]. The transverse temporal gyri (also called Heschl's gyri or Heschl's convolutions) are found in the area of primary auditory cortex in the superior temporal gyrus of the human brain, occupying Brodmann areas 41 and 42. It is the first cortical structure to process incoming auditory information. Anatomically, the transverse temporal gyri are distinct in that they run mediolaterally (towards the center of the brain) rather than dorsiventrally (front to back) as all other temporal lobe gyri run. The Heschl's gyri are named after Richard L. Heschl.
The anterior portion of the narrow middle zone between the two hemispheres of the cerebellum that is located anterior to the primary fissure
vermis of the anterior lobe of the cerebellum
The sensory system for the sense of touch and pain.
The neural tissue involved in the transmission of sensory signals
MP defines this in a may more appropriate to somatosensory cortex
The group of nerve cell bodies located on the dorsal spinal roots within the vertebral column at the level of the fourth lumbar vertebra
The neural tissue involved in the transmission of motor signals
The placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood
Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[doi: 10.1073/pnas.96.14.8138 ]
The brain ventricles or their associated choroid plexuses
TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted
The membrane between the capillary blood and alveolar air, comprised of the alveolar epithelium and the capillary epithelium and their adherent basement membranes and epithelial cell cytoplasm
The lymph tissue associated with the pharyngeal opening of the auditory tube
The posterior concave interior of the eye, consisting of the retina, the choroid, the posterior segment of the sclera, the optic disk, and blood vessels, visible by an ophthalmoscope
The anterior segment of the lamellated connective tissue layer of the cornea
The posterior segment of the lamellated connective tissue layer of the cornea
The articulation of the squamous portion of the temporal bones with the parietal bones[MP]. The squamosal suture arches backward from the pterion and connects the temporal squama with the lower border of the parietal: this suture is continuous behind with the short, nearly horizontal parietomastoid suture, which unites the mastoid process of the temporal with the region of the mastoid angle of the parietal[WP].
The part of a molar that is covered by enamel
The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins
A transparent, nearly structureless innermost layer of the choroid in contact with the pigmented layer of the retina. Bruch's membrane consists of five layers (from inside to outside): 1. the basement membrane of the retinal pigment epithelium; 2. the inner collagenous zone; 3. a central band of elastic fibers; 4. the outer collagenous zone; 5. the basement membrane of the choriocapillaris. The retinal pigment epithelium transports metabolic waste from the photoreceptors across Bruch's membrane to the choroid.
The layer of the epiphyseal plate where new bone matrix is deposited
An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP].
add more specific classification e.g. anastomosing network - consider FMA:3726
slender needle-like pointed projection that runs downward and slightly forward from the base of the inferior surface of the petrous portion of the temporal bone where it joins the tympanic portion; it gives attachment to the styloglossus, stylohyoid, and stylopharyngeus muscles and the stylohyoid and stylomandibular ligaments
styloid process of petrous part of temporal bone
The white matter fiber bundle that projects from the cingulate gyrus to the entorhinal cortex in the brain
The small parasympathetic ganglion that supplies nerve fibers to the lacrimal, nasal, palatine and pharyngeal glands
The ganglion that supplies nerve fibers to the parotid gland
the sympathetic ganglia located in front of the vertebral column and are associated with the major branches of the abdominal aorta; these include the celiac, aorticorenal, superior and inferior mesenteric ganglia
The fibers that conduct sensory nerve impulses from the viscera through the posterior dorsal roots into the spinal cord
investing bone that lies on the surface of the malleus.
To be revisted after a review of auditory ossicles
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
The lymph nodes located outside the thoracic and abdominal cavities, such as the submandibular, prescapular, axillary, inguinal and popliteal lymph nodes
blood vessels of the layer of the placenta where embryonic and maternal blood vessels interdigitate
A bone between the frontal bones in the skull; an extra bony plate within the anterior fontanelle that is not usually present
Fetally derived placental region that separates the maternal uterine tissue from the placenta labyrinth
One of the conchae of the ethmoid bone, which occupy the caudal part of the nasal fossae and form the lateral and superior portions of the turbinate bones in mammals[MP]. The ethmoturbinals are associated with the cribiform plate. They are covered with olfactory epithelium. Primarily, they serve to increase the surface area over which olfactory receptor neurons can come in contact with respiratory air. These olfactory receptor nerves then synapse with the mitral cells of the olfactory lobes through the cribiform plate in the manner described above[Palaeos]
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
internal genitalia of female reproductive system
TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
The saccular portion of the utriculosaccular duct that normally extends from the sacculus to the endolymphatic duct
The utricular portion of the utriculosaccular duct that normally extends from the utriculus to the endolymphatic duct
The utriculo-endolymphatic (UE) valve which is located in the antero-inferior wall of the utricle at the orifice of the utricular duct and serves to regulate endolymph volume in the endolymphatic sac, the utricle and the canals
One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows
primordial follicles are indiscernible to the naked eye and develop to primary, secondary, and finally mature vesicular follicles
Stage IV (690-730 microns) are oocyte maturation. Selman et al, 1993.[TAO]
A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP].
Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]
Kardong says absent in adult tetrapods, check AAO
we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally
The funnel-like expansion of the abdominal extremity of the uterine tube[MP]
The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube].
The duct that drains the anterior portion of the sublingual gland and opens at the sublingual papilla
Any of the 8-20 small ducts that open into the mouth on the surface of the sublingual fold
The small spherical bodies of epithelial cells found in the medulla of the thymus, that are arranged in a concentric pattern around clusters of degenerating lymphocytes, eosinophils and macrophages
The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells
The longitudinal groove in the midline of the anterior aspect of the medulla oblongata
anterior median fissure of medulla oblongata
fissura mediana anterior medullae oblongatae
medulla oblongata anterior median fissure
The subclasses of motor neurons which are organized into longitudinally oriented columns that occupy distinct and, in some cases, discontinuous domains along the rostrocaudal axis of the spinal cord; motor neurons within a single column send their axons to a common peripheral target
The large midline opening of the posterior inferior part of the roof of the fourth ventricle that connects the fourth ventricle to the posterior cerebromedullary cistern and the spinal cord
One of the two lateral openings of the fourth ventricle into the subarachnoid space at the cerebellopontine angle[MP].
The paired channels that connect the lateral and third ventricles and allows cerebrospinal fluid produced in the lateral ventricles to flow into the third ventricles
it is not clear if the FMA class refers to CNS or heart ventricles
The dorsal sacroiliac, the sacrotuberal and/or the iliolumbar ligaments associated with the bony ring formed by the pair of hip bones fused at the symphysis and their firm articulation with the sacrum
The irregular depression found on the posterior inner surface of the petrous portion of the temporal bone just below its crest and above and lateral to the internal acoustic meatus[MP]. In the temporal bone, above and between the aquæductus vestibuli is an irregular depression which lodges a process of the dura mater and transmits a small vein and the subarcuate artery[1] a branch of the internal auditory artery, which is an end artery that supplies blood to the inner ear ; in the infant this depression is represented by a large fossa, the subarcuate fossa, which extends backward as a blind tunnel under the superior semicircular canal. It is extensive in most primates (except for great apes) and nearly all mammals. In these animals, the subarcuate fossa houses a part of the cerebellum, the petrosal lobe[WP].
The arch that connects the lateral masses of the atlas anteriorly and articulates with the anterior articular facet of the dens of the axis[MP].
The larger and more lateral of the paired processes on either side of the hyoid bone[MP]
The greater cornua (or greater horns) of the hyoid bone project backward from the lateral borders of the body; they are flattened from above downward and diminish in size from before backward; each ends in a tubercle to which is fixed the lateral hyothyroid ligament. The upper surface is rough close to its lateral border, for muscular attachments: the largest of these are the origins of the hyoglossus and Constrictor pharyngis medius which extend along the whole length of the cornu; the digastric muscle and stylohyoid muscle have small insertions in front of these near the junction of the body with the cornu. To the medial border the hyothyroid membrane is attached, while the anterior half of the lateral border gives insertion to the thyrohyoid. The greater cornua derive from the 3rd pharyngeal arches[Wikipedia:Greater_cornu].
In humans, the greater cornua are the larger, more lateral projections from the left and right borders of the body of hyoid bone. They are in contrast to the lesser cornua, which also occur in pairs but are comparatively smaller and conical in shape. The greater cornua are derived from the third pharyngeal arches.
shorter and more medial of the paired processes on either side of the hyoid bone[MP]
The lesser cornua (or lesser horns) are two small, conical eminences, attached by their bases to the angles of junction between the body and greater cornua of the hyoid bone. They are connected to the body of the bone by fibrous tissue, and occasionally to the greater cornua by distinct diarthrodial joints, which usually persist throughout life, but occasionally become ankylosed. The lesser cornua are situated in the line of the transverse ridge on the body and appear to be morphological continuations of it. The apex of each cornu gives attachment to the stylohyoid ligament; the Chondroglossus rises from the medial side of the base. The lesser cornua are derived from the 2nd pharyngeal arches[Wikipedia:Lesser_cornu].
The main curve of the hyoid bone, from which the horns extend
A sac-like structure comprising a sebaceous gland.
cytoarchitectural part of olfactory bulb
The region of the cerebellum that is posterior to the primary fissure and anterior to the posteriolateral fissure
The region of a cerebellar lobule that resides in either of the lateral sections of the cerebellum outside the vermis; in mammals, the vermis portion of the cerebellum has a foliation pattern along the AP axis that is distinct from the lateral cerebellar hemispheres
one of the the ten gyri of the cerebellar cortex
The paired regions of the cerebellar hemisphere that lie adjacent to the vermis and are between the vermis and lateral regions of the hemispheres; it receives input from the corticopontocerebellar fibers that originate from the motor cortex, and also receives sensory feedback from the muscles; these signals are integrated by this region, to coordinate muscle activity with motor inputs
The embryonic pseudostratified epithelium of the fourth cerebellar ventricle that eventually forms the vermis and ventral neuroepithelium
The posterior portion of the narrow middle zone between the two hemispheres of the cerebellum that is located posterior to the primary fissure
vermis of the posterior lobe of the cerebellum
The sensory organ in muscle; involved in the stretch reflex and sensitive to stretch velocity
The sensory organ in muscle; involved in the stretch reflex and not sensitive to stretch velocity
The sensory organ in muscle that is involved in regulating muscle tension
The transient cup-like structure of the epiblast that consists of a single layer of embryonic cells
One of the folds of skin which form the inner lips on both sides of the vaginal opening
The normal development /maintenance of the connection between the embryo proper and extraembryonic tissues
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
The mesenchymal cells that give rise to the corneal endothelium, corneal stroma, sclera, iris stroma, ciliary muscle, ciliary stroma, and trabecular meshwork of the eye[MP].
Periocular mesenchyme (PM) is a mesencephalic neural crest derived cell population which as a result of an interaction with the retinal pigment epithelium forms the scleral cartilage of the avian eye
The sensory nerve endings in the wall of the atria of the heart, vena cava, aortic arch and carotid sinus that are sensitive to changes in blood pressure
OBSOLETE: the earliest cilia of the mouse embryo found on the cells of the embryonic node
Made obsolete as cell components are out of scope
The structure of the outer structural layer of the rodent placenta[MP].
restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition
Forms a compact layer of non-syncytial cells between the labyrinth and the outer giant cells
In the absence of direct lineage analysis, it has been assumed, from histological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP]. The eminences are found in the ventral part of the telencephalon, where they form bulges in the ventricles. These bulges develop into the basal ganglia.[1] They also contribute significantly in building up the GABAergic cortical cell population[WP].
A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the neocortex; however, hippocampal neurons, thalamus, septum and olfactory bulb neurons are also partly derived from the MGE.
A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the striatum; however, neocortex, thalamus, septum and olfactory bulb neurons are also partly derived from the LGE
The caudally located, distinct elevation of a transient proliferating cell mass of the fetal subventricular zone, located adjacent to the lateral ventricle
hat portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate.
The vascular structure encircling the anterior chamber of the eye, through which the aqueous humor is returned to the blood circulation
this vessel that receives aqueous humor from the sinus venosus sclerae (canal of Schlemm)
mesenchymal cells derived from neural crest cells that contribute to development of the hard and soft tissue in the head and neck, including the branchial arches[MP].
Ectomesenchyme has similar properties to mesenchyme. The major difference is that ectomesenchyme is usually considered to arise from neural crest cells, which are a critical group of cells that form in the cranial region during early vertebrate development. Thus, ectomesenchyme plays a critical role in the formation of the hard and soft tissues of the head and neck such as bones, muscles, teeth, and, most important, the branchial arches[Wikipedia:Ectomesenchyme].
Portion of tissue that develops from the cranial neural crest and which cells populate a series of pharyngeal arches from which develops the support skeleton of the jaw and gills[ZFA:0005771].
The thin membrane that covers the podocyte filtration slit which allows small molecules such as water, glucose, and ionic salts to pass through while retaining larger macromolecules in the bloodstream
The gaps between the interdigitated foot processes of the podocyte
The fiber-like strand of fibrillin that forms the scaffold of the cutaneous elastic fibers found in the extracellular matrix of the skin
The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate
The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects
The retinal cone cell region which contains the machinery of the cell (mitochondria, golgi, endoplasmic reticulum, etc) and where opsin molecules are assembled and passed to be part of the outer segment region
request from GO as subclass of photoreceptor segment
obsolete retinal cone cell inner segment
The retinal cone cell region in which the visual pigment rhodopsin is in invaginations of the cell membrane
obsolete retinal cone cell outer segment
The retinal rod cell region which contains the machinery of the cell (mitochondria, golgi, endoplasmic reticulum, etc) and where opsin molecules are assembled and passed to be part of the outer segment region
The retinal rod cell region which contains stacks of membranous discs separate from the outer cell membrane that are rich in the visual pigment rhodopsin
The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone
The nodules of small undifferentiated B lymphocytes and follicular dendritic cells located in the spleen white pulp
FMA:15843 is classified as primary follicle so it belongs here
The nodules of antigen-activated, differentiating B cells, follicular dendritic cells, antigen-presenting T cells and macrophages in the spleen white pulp
The spherical enlargement at the base of each semicircular canal where they connect with the utricle, containing the crista ampullaris which detects movement of the fluid within the canals
TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as 'ampulla of anterior semicircular canal'
membraneous ampulla of the semicircular duct
The extraembryonic tissue that is responsible for the proper orientation of the anterior-posterior axis of the embryo and for appropriate patterning of adjacent embryonic tissue
The extension of the hindgut of the primitive digestive tube of the embryo, caudal to the location of the anal opening
The mesendoderm which first migrates from the node and which gives rise to the gut
The enclosed space where the arachnoid membrane stretches between the two temporal lobes and encloses the cerebral peduncles including the structures contained in the interpeduncular fossa
The space located on lateral aspects of the pons at the junction with the celebellum
The largest of the subarachnoid cisterns between the cerebellum and the medulla oblongata; it is divided into a posterior cerebellomedullary cistern [TA] located between the cerebellum and the posterior surface of the medulla (also called cisterna magna), and a lateral cerebellomedullary cistern [TA] located between the cerebellum and the lateral aspect of the medulla.
The widening portions of the subarachnoid space within the cranium where the arachnoid bridges over a depression on the surface of the brain
in FMA is a subdivision of arachnoid space
The space between the cerebellum and the lateral aspect of the medulla
The enclosed space extending forward between the corpus callosum and the thalamus that contains the internal cerebral veins
The external masculine genital organs, including the penis and scrotum
The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands
consider splitting genitalia from genital organ
The small depression in the primitive streak that is caudal to the primitive node where the cells of the epiblast initially begin to invaginate during early embryogenesis
The primitive pit is a depression in the center of the primitive node, connecting to the notochord. It consists of part of the primitive streak[Wikipedia:Primitive_pit].
The shallow valley that extends along the length of the primitive streak[MP]
A shallow groove, the primitive groove, appears on the surface of the primitive streak, and the anterior end of this groove communicates by means of an aperture, the blastophore, with the yolk-sac[Wikipedia:Primitive_groove].
The skeletal muscle fiber structure comprised of the transverse tubule and the two associated terminal cisternae; each fiber normally has thousands of triads
One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]
In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule)
The subclasses of motor neurons which project their axons to axial muscles that lie close to the vertebral column; motor neurons in the lateral subdivision of the MMC project their axons to body wall muscles
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
The region of the mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses; the alar plate develops into the dorsal horn in the grey matter of the spinal cord
TODO - merge with UBERON:0003054 roof plate?
The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons.
The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout.
The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it
The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it
Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity.
The forebrain region that coordinates sensory signaling arising from the vomeronasal organ; it is located on the dorsal-posterior portion of the main olfactory bulb, and the axons that leave the accessory olfactory bulb project to targets in the amygdala and hypothalamus
NIFSTD:nlx_anat_20090453 appears to be retired
Projection notes: Site of termination of vomeronasal nerve; projects to: other parts of pallial amygdala, medial amygdala, subpallial nucleus (Butler and Hodos)
The region of a cerebellar lobule that resides in the central section of the cerebellum between the two hemispheres;
in humans, vermis lobule regions may be nearly continuous with the cerebellar hemisphere lobules dorsally but are separated by deeper longitudinal fissues in the ventral regions; in mammals, the vermis portion of the cerebellum has a foliation pattern along the AP axis that is distinct from the lateral cerebellar hemispheres
The two or three small masses of gray matter that is located medial to the emboliform nucleus and lateral to the fastigial nucleus; it receives axons from the intermediate area of the cerebellar hemispheres and its afferents exit through the superior cerebellar peduncle.
it is recognized in human cerebellum but is not distinguishable in all mammalian species[MP]
The nucelus composed of the globose and emoliform nuclei of the cerebellum; in some mammalian species the globose nucleus is not distinguishable
TODO FMA:61904 lingual gyrus FMA:71032 lingula gyrus (lg)
central vs alar central? II and III? part_of CENT in ABA
The culmen is the portion of the anterior vermis adjacent to the primary fissure of cerebellum. The culmen and the anterior parts of the quadrangular lobules form the lobus culminis[WP].
lobule IX of cerebellar posterior vermis
The uvula is the second largest lobule, following the culmen. It pertains to the paleocerebellum and is separated from the nodule by the posterolateral fissure.
lobule V (culmen and quadrangular lobule, posterior part)
The folium vermis is a short, narrow, concealed band at the posterior extremity of the vermis, consisting apparently of a single folium, but in reality marked on its upper and under surfaces by secondary fissures. Laterally, it expands in either hemisphere into a considerable lobule, the superior semilunar lobule (lobulus semilunaris superior; postero-superior lobules), which occupies the posterior third of the upper surface of the hemisphere, and is bounded below by the horizontal sulcus. The superior semilunar lobules and the folium vermis form the lobus semilunaris.
One of the folds of skin which form the inner lips (labia minora) and outer lips (labia majora) on both sides of the vaginal opening.
One of the folds of skin which form the outer lips on both sides of the vaginal opening
one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid
Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[NIFSTD:birnlex_1356].
FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies.
Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
The middle of the face including the nose and its associated bony structures[MW].
this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface.
does not contain any subparts in FMA. In HP covers eyelid, eyebrow, soft tissue
The toothlike process on the upper surface of the axis, which articulates with the atlas above[GAID].
TODO check AAO:0000721 odontoid_process -- Anterior process located between the atlantal cotyles that projects into the foramen magnum of the skull and bears facets that articulate with the lateral walls of the foramen
Anterior process located between the atlantal cotyles that projects into the foramen magnum of the skull and bears facets that articulate with the lateral walls of the foramen.[AAO]
Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint.
The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone.
one of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP].
Anatomical line demarcating the boundary between forehead and scalp.
horizontal piece of cartilage located outside the ear canal that divides the upper and lower parts of the ear.
crus of helical part of auricular cartilage
Part of the cranium, the clivus is a shallow depression behind the dorsum sellC& that slopes obliquely backward. It forms a gradual sloping process at the anterior most portion of the basilar occipital bone at its junction with the sphenoid bone. On axial planes, it sits just posterior to the sphenoid sinuses. Just lateral to the clivus bilaterally is the foramen lacerum which contains the internal carotid artery, proximal to its anastamosis with the Circle of Willis. Posterior to the clivus is the basilar artery. The clivus supports the upper part of the pons.
The clivus is an important landmark for checking for anatomical atlanto-occipital alignment; the clivus, when viewed on a lateral C-spine X-ray, forms a line which, if extended, is known as Wackenheim's clivus line. Wackenheim's clivus line should pass through the dens of the axis or be tangential to it.
The outer or sperficial part of the humerus.
An anatomical cavity that is the combination of the cavity between the nares and the choanae[HP,modified].
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
A muscle of the tympanic cavity that attaches to an auditory ossicle.
attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter
small cavity surrounding the bones of the middle ear.
A blood vessel that is part of a tympanic cavity [Automatically generated definition].
anatomical cavity of middle ear blood vessel
blood vessel of anatomical cavity of middle ear
blood vessel of middle ear anatomical cavity
middle ear anatomical cavity blood vessel
A nerve that is part of a tympanic cavity [Automatically generated definition].
nerve of anatomical cavity of middle ear
An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches.
Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO]
The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389]
A vasculature that is part of a iris [Automatically generated definition].
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
An organ component layer that is part of a myocardium.
The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA].
The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO]
outer dense layer of the myocardium uniting the epicardium and myocardium[MP].
A myocardium trabecular layer that is part of a cardiac ventricle.
The outer layer the ventricular myocardium, muscle fibers are arranged in a compact form and involved the entire ventricle.
The outer layer the ventricular myocardium, muscle fibers are arranged in a compact form and involved the entire ventricle.[TAO]
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo.
cytoarchitectural part of the cerebellar cortex
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. The nucleus is divided into three parts, from rostral to caudal (top to bottom in humans): * The mesencephalic nucleus * The chief sensory nucleus (or pontine nucleus or main sensory nucleus or primary nucleus) * The spinal trigeminal nucleus[WP].
TODO - check ZFA link. note this is part of medulla in ZFA, but we do not include this link here as it leads to inconsistencies
In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].
TODO - ensure definition works across species.
The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments
The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules
TODO - check for applicability across species
The somitomeric trunk muscle is derived from somitomeric mesoderm. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. An example of this process is found in Mus musculus.[GO].
TODO - find N+S conditions. SMT & develops_from somite is not specific enough (all SMT develops_from somite)
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
The outflow tract septum is a partition in the outflow tract
The outflow tract is the portion of the heart through which blood flows into the arteries
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles
Vein of heart that drains the myocardium
A heart valve located between the ventricle and bulbus arteriosus.
Vestigial cardiac valve which is continuous with the valve of the inferior vena cava[FMA].
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
The bulbus arteriosus is an elastic heart chamber[GO]. Multi-tissue structure that consists of three layers and through which the blood exits the heart. The bulbus arteriosus is a pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches[ZFA].
A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]
replaces conus arteriosis in cartilaginous fish
Endocardial cushions project into the atrial canal, and, meeting in the middle line, unite to form the septum intermedium which divides the canal into two channels, the future right and left atrioventricular orifices[Gray's via WP].
In the developing heart, the cavity of the primitive atrium becomes subdivided into right and left chambers by a septum, the septum primum, which grows downward into the cavity. The increasingly smaller gap below it (before it fuses with the endocardial cushion) is known as the ostium primum. The septum primum eventually fuses with the endocardial cushion, closing the ostium primum off completely. Meanwhile, perforations appear in the superior part of the septum primum, forming the ostium secundum. This will eventually form part of the fossa ovalis.
The first of the two membranous sheets which partially separate the two atria during embryonic development. [TFD][VHOG]
The second of the two membranous sheets which partially separate the two atria during embryonic development. [TFD][VHOG]
The septum secundum, semilunar in shape, grows downward from the upper wall of the atrium immediately to the right of the primary septum and ostium secundum. Shortly after birth it fuses with the septum primum, and consequently the foramen ovale is closed, but sometimes the fusion is incomplete and the upper part of the foramen remains patent. The limbus fossae ovalis denotes the free margin of the septum secundum.
An outpouching of the septum transversum[GO]. An embryonic group of progenitor cells that forms near the venous pole of the heart and gives rise to the epicardium[Wiktionary]
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
The pulmonary myocardium is the myocardial tissue present in the pulmonary vein
portions of the midgut that are derived from ectoderm.
A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves.
The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707].
check ZFA structures superior reticular formation medial column & tegmentum
The region of the cerebral cortex covering the basal surface of the frontal lobes; this region normally controls emotion and decision making
The band of nerve fibers which cross the midline of the spinal cord ventral to the central canal and posterior grey commissure[MP]. The anterior (or ventral) white commissure, also known as the alba anterior medullae spinalis, is a bundle of nerve fibers which cross the midline of the spinal cord just anterior to the gray commissure. A N4 fibers and C fibers carrying pain sensation in the spinothalamic tract contribute to this commissure, as do fibers of the anterior corticospinal tract, which carry motor signals from the primary motor cortex[WP].
anterior white commissure of spinal cord
commissura alba anterior medullae spinalis
The trigeminothalamic tract is one of the major routes of nociceptive and temperature signaling from the face
Axon tract that carries efferent (outgoing) action potentials from the cell body in the pons towards target cells in the spinal cord.
Axon tract that carries efferent (outgoing) action potentials from the cell body in the medulla towards target cells in the spinal cord[GO].
Joint in the leg. For example the knee, which separates the leg tibia and femur
Originally created for consistenct with GO, obsoleted when the GO class was obsoleted as the meaning was unclear
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
the nonstriated, involuntary muscle tissue located in the wall of the aorta
A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells
Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]
The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts
Mammary gland cords form when the mammary gland bud invades the mammary fat
The embryonic vessels grow through the layer to come in close contact with the maternal blood supply
blood vessel of labyrinthine layer of placenta
labyrinthine layer of placenta blood vessel
The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland
TODO - check also FMA Stroma of glandular part of prostate
A portions of the gut that is derived from endoderm.
The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer
NIF divides this into main and accessory
olfactory bulb main mitral cell body layer
The Harderian gland is an anterior orbital gland usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species[GO].
In mouse the HG appears in the posterior part of eye region, in the form of nonluminated tubules between the sixteenth and eighteenth days of gestation. At birth it is still not differentiated histologically. In birds the HG originates from the conjunctival epithelium at a late embryonic stage. In the English sparrow, Passer domesticus (incubation period of about 13 days), it appears between the seventh and the eighth days of incubation. In the chick embryo (incubation period of about 21 days) it originates between the eleventh and the twelfth days.[PMID:9156609]
In the limbless, burrowing amphibian Apoda (Caecilians) the harderian gland is very large, filling much of the orbit and lubricating a retractile sensory tentacle rather than the eye (Walls, 1942; Wolff, 1948).
In mammals, the gland excretes an oily substance used to preen the fur[WP]
In some animals it acts as an accessory to the lacrimal gland, secreting fluid that eases movement of the nictitating membrane[WP]
The functions attributed to the gland are many and diverse. Amongst these, it has been held to be a site of immune responses, a source of thermoregulatory lipids, a source of pheromones, a photoprotective organ and part of a retinal-pineal axis. It is arguably the last remaining large organ of widespread dis- tribution among the vertebrates to which we cannot confidently ascribe a confirmed function.
The harderian gland may be compound tubular (MacLeod, 1880; Paule, 1957) or compound tubuloacinar/tubuloalveolar (Aureli, 1957; Hoffman, 1971).
The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.
TODO - check - GO says outer, BTO says inner. Make this a superclass
The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus
The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus
A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water
ascending limb thin segment of loop of Henle
loop of Henle ascending limb thin segment
Long nephrons are associated with juxtamedullary glomeruli and extend to the inner medulla
Short nephrons are associated with mid-cortical glomeruli, and have no short ascending limb, so the limb is situated in the outer medulla
The S1 portion is the initial portion of the proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO].
The S2 portion of the tubule is involved in reabsorption of water and sodium chloride[GO].
The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron
The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron
Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.
not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)
The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules
The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules
The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex
The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla
The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla
The long descending thin limb bend is a part of the descending thin limb of a long nephron that lies beyond the prebend segment
The prebend segment is a part of the descending thin limb that lies before the bend and exhibits robust sodium chloride reabsorption
Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron
The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman’s capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman’s capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman’s capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]
The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.
note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap
The nephron epithelium is a tissue that covers the surface of a nephron
the small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus
Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]
A nerve that is part of a hindlimb stylopod [Automatically generated definition].
Proximal segment of free lower limb nerve
nerve of Proximal segment of free lower limb
A nerve that is part of a back [Automatically generated definition].
A nerve that is part of a lower arm [Automatically generated definition].
brachial region middle limb segment nerve
intermediate segment of free upper limb nerve
middle limb segment of brachial region nerve
middle limb segment of proximal segment of free upper limb nerve
nerve of brachial region middle limb segment
nerve of intermediate segment of free upper limb
nerve of middle limb segment of brachial region
nerve of middle limb segment of proximal segment of free upper limb
nerve of proximal segment of free upper limb middle limb segment
nerve of proximal segment of free upper limb zeugopod
nerve of zeugopod of proximal segment of free upper limb
proximal segment of free upper limb middle limb segment nerve
proximal segment of free upper limb zeugopod nerve
zeugopod of proximal segment of free upper limb nerve
A nerve that is part of a forelimb stylopod [Automatically generated definition].
nerve of proximal segment of free upper limb stylopod
nerve of stylopod of proximal segment of free upper limb
proximal segment of free upper limb stylopod nerve
stylopod of proximal segment of free upper limb nerve
A nerve that is part of a lower leg [Automatically generated definition].
inferior member middle limb segment nerve
intermediate segment of free lower limb nerve
lower extremity middle limb segment nerve
middle limb segment of inferior member nerve
middle limb segment of lower extremity nerve
nerve of inferior member middle limb segment
nerve of intermediate segment of free lower limb
nerve of lower extremity middle limb segment
nerve of middle limb segment of hind limb
nerve of middle limb segment of hindlimb
nerve of middle limb segment of inferior member
nerve of middle limb segment of lower extremity
A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition].
A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition].
MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa
A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition].
A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition].
A muscular coat that is part of a vas deferens [Automatically generated definition].
TODO - check MA and FMA classes mean the same thing
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius involuntary muscle
apparatus respiratorius non-striated muscle
apparatus respiratorius smooth muscle tissue
involuntary muscle of apparatus respiratorius
involuntary muscle of respiratory system
non-striated muscle of apparatus respiratorius
non-striated muscle of respiratory system
smooth muscle of apparatus respiratorius
smooth muscle tissue of apparatus respiratorius
smooth muscle tissue of respiratory system
A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition].
gastrointestinal system involuntary muscle
gastrointestinal system non-striated muscle
gastrointestinal system smooth muscle tissue
involuntary muscle of gastrointestinal system
non-striated muscle of gastrointestinal system
smooth muscle of gastrointestinal system
smooth muscle tissue of digestive system
smooth muscle tissue of gastrointestinal system
the smooth muscle tissue surrounding the urothelium of the kidney pelvis
A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition].
A portion of smooth muscle tissue that is part of a trigone of urinary bladder [Automatically generated definition].
involuntary muscle of Lieutaud's trigone
involuntary muscle of trigone of bladder
involuntary muscle of trigone of urinary bladder
involuntary muscle of urinary bladder trigone
non-striated muscle of Lieutaud's trigone
non-striated muscle of trigone of bladder
non-striated muscle of trigone of urinary bladder
non-striated muscle of urinary bladder trigone
smooth muscle of trigone of urinary bladder
smooth muscle of urinary bladder trigone
smooth muscle tissue of Lieutaud's trigone
smooth muscle tissue of trigone of bladder
smooth muscle tissue of trigone of urinary bladder
smooth muscle tissue of urinary bladder trigone
trigone of urinary bladder involuntary muscle
trigone of urinary bladder non-striated muscle
trigone of urinary bladder smooth muscle
trigone of urinary bladder smooth muscle tissue
urinary bladder trigone involuntary muscle
urinary bladder trigone non-striated muscle
urinary bladder trigone smooth muscle tissue
A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition].
involuntary muscle of neck of urinary bladder
involuntary muscle of urinary bladder neck
neck of urinary bladder involuntary muscle
neck of urinary bladder non-striated muscle
neck of urinary bladder smooth muscle tissue
non-striated muscle of neck of urinary bladder
non-striated muscle of urinary bladder neck
smooth muscle of neck of urinary bladder
smooth muscle tissue of neck of urinary bladder
smooth muscle tissue of urinary bladder neck
urinary bladder neck non-striated muscle
urinary bladder neck smooth muscle tissue
A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum involuntary muscle
anal part of perineum non-striated muscle
anal part of perineum smooth muscle tissue
involuntary muscle of anal part of perineum
non-striated muscle of anal part of perineum
smooth muscle tissue of anal part of perineum
A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition].
smooth muscle tissue of lymphatic vessel
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
involuntary muscle of lower respiratory tract
lower respiratory tract involuntary muscle
lower respiratory tract non-striated muscle
lower respiratory tract smooth muscle tissue
non-striated muscle of lower respiratory tract
smooth muscle of lower respiratory tract
smooth muscle tissue of lower respiratory tract
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
A portion of smooth muscle tissue that is part of a mammary gland [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition].
A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition].
A portion of smooth muscle tissue that is part of a main bronchus [Automatically generated definition].
bronchus principalis non-striated muscle
bronchus principalis smooth muscle tissue
involuntary muscle of bronchus principalis
involuntary muscle of principal bronchus
non-striated muscle of bronchus principalis
non-striated muscle of principal bronchus
smooth muscle tissue of bronchus principalis
smooth muscle tissue of primary bronchus
smooth muscle tissue of principal bronchus
A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition].
A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition].
A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition].
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
A bone that is part of the dorsal region of an animal.
this class may be obsoleted. See: https://sourceforge.net/p/obo/mouse-anatomy-requests/79/
A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids.
A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids.
A bone that is part of a forelimb stylopod [Automatically generated definition].
May be merged into humerus. See: https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376
A bone that is part of a lower leg [Automatically generated definition].
bone of inferior member middle limb segment
bone of intermediate segment of free lower limb
bone of lower extremity middle limb segment
bone of middle limb segment of hind limb
bone of middle limb segment of inferior member
bone of middle limb segment of lower extremity
bone organ of hind limb middle limb segment
bone organ of hindlimb middle limb segment
bone organ of inferior member middle limb segment
bone organ of intermediate segment of free lower limb
bone organ of lower extremity middle limb segment
bone organ of middle limb segment of hind limb
bone organ of middle limb segment of hindlimb
bone organ of middle limb segment of inferior member
bone organ of middle limb segment of lower extremity
bone organ of zeugopod of inferior member
bone organ of zeugopod of lower extremity
hind limb middle limb segment bone organ
inferior member middle limb segment bone
inferior member middle limb segment bone organ
intermediate segment of free lower limb bone
intermediate segment of free lower limb bone organ
lower extremity middle limb segment bone
lower extremity middle limb segment bone organ
middle limb segment of hind limb bone organ
middle limb segment of hindlimb bone organ
middle limb segment of inferior member bone
middle limb segment of inferior member bone organ
middle limb segment of lower extremity bone
middle limb segment of lower extremity bone organ
A muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition].
A muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
A muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition].
A muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition].
the FMA class 'muscle of arm' belongs here, do not move
See notes on UBERON:0001460 for possible terminological confusion over term 'arm'
A muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition].
the FMA class 'muscle of leg' belongs here, do not move
See notes on UBERON:0000978 for possible terminological confusion over term 'leg'
A blood vessel that is part of a hindlimb stylopod [Automatically generated definition].
A blood vessel that is part of a back [Automatically generated definition].
A blood vessel that is part of a lower arm [Automatically generated definition].
A blood vessel that is part of a forelimb stylopod [Automatically generated definition].
A blood vessel that is part of a lower leg [Automatically generated definition].
A zone of skin that is part of a hindlimb stylopod [Automatically generated definition].
Proximal segment of free lower limb skin
skin of Proximal segment of free lower limb
A zone of skin that is part of a forelimb stylopod [Automatically generated definition].
proximal segment of free upper limb stylopod skin
skin of proximal segment of free upper limb stylopod
skin of stylopod of proximal segment of free upper limb
stylopod of proximal segment of free upper limb skin
A zone of skin that is part of a lower leg [Automatically generated definition].
inferior member middle limb segment skin
intermediate segment of free lower limb skin
lower extremity middle limb segment skin
middle limb segment of inferior member skin
middle limb segment of lower extremity skin
skin of inferior member middle limb segment
skin of intermediate segment of free lower limb
skin of lower extremity middle limb segment
skin of middle limb segment of hind limb
skin of middle limb segment of inferior member
skin of middle limb segment of lower extremity
A myocardium that is part of a outflow tract [Automatically generated definition].
(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]
A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition].
Proximal segment of free lower limb connective tissue
Proximal segment of free lower limb portion of connective tissue
Proximal segment of free lower limb textus connectivus
connective tissue of Proximal segment of free lower limb
connective tissue of inferior member stylopod
connective tissue of lower extremity stylopod
connective tissue of stylopod of hind limb
connective tissue of stylopod of hindlimb
connective tissue of stylopod of inferior member
connective tissue of stylopod of lower extremity
connective tissue of stylopod of lower limb
hind limb stylopod portion of connective tissue
hindlimb stylopod portion of connective tissue
inferior member stylopod connective tissue
inferior member stylopod portion of connective tissue
inferior member stylopod textus connectivus
lower extremity stylopod connective tissue
lower extremity stylopod portion of connective tissue
lower extremity stylopod textus connectivus
portion of connective tissue of Proximal segment of free lower limb
portion of connective tissue of hind limb stylopod
portion of connective tissue of hindlimb stylopod
portion of connective tissue of inferior member stylopod
portion of connective tissue of lower extremity stylopod
portion of connective tissue of stylopod of hind limb
portion of connective tissue of stylopod of hindlimb
portion of connective tissue of stylopod of inferior member
portion of connective tissue of stylopod of lower extremity
portion of connective tissue of stylopod of lower limb
portion of connective tissue of upper leg
stylopod of hind limb portion of connective tissue
stylopod of hind limb textus connectivus
stylopod of hindlimb portion of connective tissue
stylopod of inferior member connective tissue
stylopod of inferior member portion of connective tissue
stylopod of inferior member textus connectivus
stylopod of lower extremity connective tissue
stylopod of lower extremity portion of connective tissue
stylopod of lower extremity textus connectivus
stylopod of lower limb connective tissue
stylopod of lower limb portion of connective tissue
stylopod of lower limb textus connectivus
textus connectivus of Proximal segment of free lower limb
textus connectivus of hind limb stylopod
textus connectivus of inferior member stylopod
textus connectivus of lower extremity stylopod
textus connectivus of stylopod of hind limb
textus connectivus of stylopod of hindlimb
textus connectivus of stylopod of inferior member
textus connectivus of stylopod of lower extremity
textus connectivus of stylopod of lower limb
A portion of connective tissue that is part of a back [Automatically generated definition].
A portion of connective tissue that is part of a lower arm [Automatically generated definition].
antebrachial region portion of connective tissue
arm middle limb segment connective tissue
arm middle limb segment portion of connective tissue
arm middle limb segment textus connectivus
arm zeugopod portion of connective tissue
brachial region middle limb segment connective tissue
brachial region middle limb segment portion of connective tissue
brachial region middle limb segment textus connectivus
brachial region zeugopod connective tissue
brachial region zeugopod portion of connective tissue
brachial region zeugopod textus connectivus
connective tissue of antebrachial region
connective tissue of arm middle limb segment
connective tissue of brachial region middle limb segment
connective tissue of brachial region zeugopod
connective tissue of intermediate segment of free upper limb
connective tissue of lower segment of arm
connective tissue of middle limb segment of arm
connective tissue of middle limb segment of brachial region
connective tissue of middle limb segment of proximal segment of free upper limb
connective tissue of proximal segment of free upper limb middle limb segment
connective tissue of proximal segment of free upper limb zeugopod
connective tissue of zeugopod of brachial region
connective tissue of zeugopod of proximal segment of free upper limb
intermediate segment of free upper limb connective tissue
intermediate segment of free upper limb portion of connective tissue
intermediate segment of free upper limb textus connectivus
lower segment of arm portion of connective tissue
middle limb segment of arm connective tissue
middle limb segment of arm portion of connective tissue
middle limb segment of arm textus connectivus
middle limb segment of brachial region connective tissue
middle limb segment of brachial region portion of connective tissue
middle limb segment of brachial region textus connectivus
middle limb segment of proximal segment of free upper limb connective tissue
middle limb segment of proximal segment of free upper limb portion of connective tissue
middle limb segment of proximal segment of free upper limb textus connectivus
portion of connective tissue of antebrachial region
portion of connective tissue of arm middle limb segment
portion of connective tissue of arm zeugopod
portion of connective tissue of brachial region middle limb segment
portion of connective tissue of brachial region zeugopod
portion of connective tissue of intermediate segment of free upper limb
portion of connective tissue of lower arm
portion of connective tissue of lower segment of arm
portion of connective tissue of middle limb segment of arm
portion of connective tissue of middle limb segment of brachial region
portion of connective tissue of middle limb segment of proximal segment of free upper limb
portion of connective tissue of proximal segment of free upper limb middle limb segment
portion of connective tissue of proximal segment of free upper limb zeugopod
portion of connective tissue of zeugopod of arm
portion of connective tissue of zeugopod of brachial region
portion of connective tissue of zeugopod of proximal segment of free upper limb
proximal segment of free upper limb middle limb segment connective tissue
proximal segment of free upper limb middle limb segment portion of connective tissue
proximal segment of free upper limb middle limb segment textus connectivus
proximal segment of free upper limb zeugopod connective tissue
proximal segment of free upper limb zeugopod portion of connective tissue
proximal segment of free upper limb zeugopod textus connectivus
textus connectivus of antebrachial region
textus connectivus of arm middle limb segment
textus connectivus of brachial region middle limb segment
textus connectivus of brachial region zeugopod
textus connectivus of intermediate segment of free upper limb
textus connectivus of lower segment of arm
textus connectivus of middle limb segment of arm
textus connectivus of middle limb segment of brachial region
textus connectivus of middle limb segment of proximal segment of free upper limb
textus connectivus of proximal segment of free upper limb middle limb segment
textus connectivus of proximal segment of free upper limb zeugopod
textus connectivus of zeugopod of brachial region
textus connectivus of zeugopod of proximal segment of free upper limb
zeugopod of arm portion of connective tissue
zeugopod of brachial region connective tissue
zeugopod of brachial region portion of connective tissue
zeugopod of brachial region textus connectivus
zeugopod of proximal segment of free upper limb connective tissue
zeugopod of proximal segment of free upper limb portion of connective tissue
zeugopod of proximal segment of free upper limb textus connectivus
A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition].
arm stylopod portion of connective tissue
brachial region stylopod connective tissue
brachial region stylopod portion of connective tissue
brachial region stylopod textus connectivus
connective tissue of brachial region stylopod
connective tissue of proximal segment of free upper limb stylopod
connective tissue of stylopod of brachial region
connective tissue of stylopod of proximal segment of free upper limb
portion of connective tissue of arm stylopod
portion of connective tissue of brachial region stylopod
portion of connective tissue of proximal segment of free upper limb stylopod
portion of connective tissue of stylopod of arm
portion of connective tissue of stylopod of brachial region
portion of connective tissue of stylopod of proximal segment of free upper limb
portion of connective tissue of upper arm
proximal segment of free upper limb stylopod connective tissue
proximal segment of free upper limb stylopod portion of connective tissue
proximal segment of free upper limb stylopod textus connectivus
stylopod of arm portion of connective tissue
stylopod of brachial region connective tissue
stylopod of brachial region portion of connective tissue
stylopod of brachial region textus connectivus
stylopod of proximal segment of free upper limb connective tissue
stylopod of proximal segment of free upper limb portion of connective tissue
stylopod of proximal segment of free upper limb textus connectivus
textus connectivus of brachial region stylopod
textus connectivus of proximal segment of free upper limb stylopod
textus connectivus of stylopod of brachial region
textus connectivus of stylopod of proximal segment of free upper limb
A portion of connective tissue that is part of a lower leg [Automatically generated definition].
connective tissue of hind limb middle limb segment
connective tissue of hindlimb middle limb segment
connective tissue of inferior member middle limb segment
connective tissue of inferior member zeugopod
connective tissue of intermediate segment of free lower limb
connective tissue of lower extremity middle limb segment
connective tissue of lower extremity zeugopod
connective tissue of middle limb segment of hind limb
connective tissue of middle limb segment of hindlimb
connective tissue of middle limb segment of inferior member
connective tissue of middle limb segment of lower extremity
connective tissue of zeugopod of hind limb
connective tissue of zeugopod of hindlimb
connective tissue of zeugopod of inferior member
connective tissue of zeugopod of lower extremity
hind limb middle limb segment connective tissue
hind limb middle limb segment portion of connective tissue
hind limb middle limb segment textus connectivus
hind limb zeugopod portion of connective tissue
hindlimb middle limb segment connective tissue
hindlimb middle limb segment portion of connective tissue
hindlimb middle limb segment textus connectivus
hindlimb zeugopod portion of connective tissue
inferior member middle limb segment connective tissue
inferior member middle limb segment portion of connective tissue
inferior member middle limb segment textus connectivus
inferior member zeugopod connective tissue
inferior member zeugopod portion of connective tissue
inferior member zeugopod textus connectivus
intermediate segment of free lower limb connective tissue
intermediate segment of free lower limb portion of connective tissue
intermediate segment of free lower limb textus connectivus
lower extremity middle limb segment connective tissue
lower extremity middle limb segment portion of connective tissue
lower extremity middle limb segment textus connectivus
lower extremity zeugopod connective tissue
lower extremity zeugopod portion of connective tissue
lower extremity zeugopod textus connectivus
middle limb segment of hind limb connective tissue
middle limb segment of hind limb portion of connective tissue
middle limb segment of hind limb textus connectivus
middle limb segment of hindlimb connective tissue
middle limb segment of hindlimb portion of connective tissue
middle limb segment of hindlimb textus connectivus
middle limb segment of inferior member connective tissue
middle limb segment of inferior member portion of connective tissue
middle limb segment of inferior member textus connectivus
middle limb segment of lower extremity connective tissue
middle limb segment of lower extremity portion of connective tissue
middle limb segment of lower extremity textus connectivus
portion of connective tissue of hind limb middle limb segment
portion of connective tissue of hind limb zeugopod
portion of connective tissue of hindlimb middle limb segment
portion of connective tissue of hindlimb zeugopod
portion of connective tissue of inferior member middle limb segment
portion of connective tissue of inferior member zeugopod
portion of connective tissue of intermediate segment of free lower limb
portion of connective tissue of lower extremity middle limb segment
portion of connective tissue of lower extremity zeugopod
portion of connective tissue of lower leg
portion of connective tissue of middle limb segment of hind limb
portion of connective tissue of middle limb segment of hindlimb
portion of connective tissue of middle limb segment of inferior member
portion of connective tissue of middle limb segment of lower extremity
portion of connective tissue of zeugopod of hind limb
portion of connective tissue of zeugopod of hindlimb
portion of connective tissue of zeugopod of inferior member
portion of connective tissue of zeugopod of leg
portion of connective tissue of zeugopod of lower extremity
textus connectivus of hind limb middle limb segment
textus connectivus of hind limb zeugopod
textus connectivus of hindlimb middle limb segment
textus connectivus of inferior member middle limb segment
textus connectivus of inferior member zeugopod
textus connectivus of intermediate segment of free lower limb
textus connectivus of lower extremity middle limb segment
textus connectivus of lower extremity zeugopod
textus connectivus of middle limb segment of hind limb
textus connectivus of middle limb segment of hindlimb
textus connectivus of middle limb segment of inferior member
textus connectivus of middle limb segment of lower extremity
textus connectivus of zeugopod of hind limb
textus connectivus of zeugopod of hindlimb
textus connectivus of zeugopod of inferior member
textus connectivus of zeugopod of lower extremity
zeugopod of hind limb portion of connective tissue
zeugopod of hind limb textus connectivus
zeugopod of hindlimb portion of connective tissue
zeugopod of inferior member connective tissue
zeugopod of inferior member portion of connective tissue
zeugopod of inferior member textus connectivus
zeugopod of leg portion of connective tissue
zeugopod of lower extremity connective tissue
zeugopod of lower extremity portion of connective tissue
zeugopod of lower extremity textus connectivus
A pericardium that is part of a outflow tract [Automatically generated definition].
A cranial suture that is part of a cartilaginous joint [Automatically generated definition].
articulatio cartilaginea cranial sutures
articulatio cartilaginea cranial sutures set
articulatio cartilaginea suture of cranium
cranial suture of articulatio cartilaginea
cranial sutures of articulatio cartilaginea
cranial sutures set of articulatio cartilaginea
cranial sutures set of cartilaginous joint
cranium suture of articulatio cartilaginea
suture of cranium of articulatio cartilaginea
suture of cranium of cartilaginous joint
A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle
chorioid plexus of cerebral hemisphere epithelium of lateral ventricle
choroid plexus epithelial tissue of lateral ventricle
choroid plexus epithelium of lateral ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle
epithelial tissue of choroid plexus of lateral ventricle
epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle
epithelium of choroid plexus of lateral ventricle
lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue
lateral ventricle chorioid plexus of cerebral hemisphere epithelium
lateral ventricle choroid plexus epithelial tissue
lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
lateral ventricle epithelial tissue of choroid plexus
lateral ventricle epithelium of chorioid plexus of cerebral hemisphere
lateral ventricle epithelium of choroid plexus
lateral ventricle choroid plexus epithelium
A choroid plexus epithelium that is part of a third ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of third ventricle
chorioid plexus of cerebral hemisphere epithelium of third ventricle
choroid plexus epithelial tissue of third ventricle
choroid plexus epithelium of third ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of third ventricle
epithelial tissue of choroid plexus of third ventricle
epithelium of chorioid plexus of cerebral hemisphere of third ventricle
epithelium of choroid plexus of third ventricle
third ventricle chorioid plexus of cerebral hemisphere epithelial tissue
third ventricle chorioid plexus of cerebral hemisphere epithelium
third ventricle choroid plexus epithelial tissue
third ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
third ventricle epithelial tissue of choroid plexus
third ventricle epithelium of chorioid plexus of cerebral hemisphere
third ventricle epithelium of choroid plexus
third ventricle choroid plexus epithelium
A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle
chorioid plexus of cerebral hemisphere epithelium of fourth ventricle
choroid plexus epithelial tissue of fourth ventricle
choroid plexus epithelium of fourth ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle
epithelial tissue of choroid plexus of fourth ventricle
epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle
epithelium of choroid plexus of fourth ventricle
fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue
fourth ventricle chorioid plexus of cerebral hemisphere epithelium
fourth ventricle choroid plexus epithelial tissue
fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
fourth ventricle epithelial tissue of choroid plexus
fourth ventricle epithelium of chorioid plexus of cerebral hemisphere
fourth ventricle epithelium of choroid plexus
fourth ventricle choroid plexus epithelium
A muscle that is part of the eye region.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
An anatomical structure found in mollusks and used for feeding. It is a minutely toothed, chitinous ribbon. It is typically used for scraping or cutting food before the food enters the esophagus. The radula is unique to the molluscs, and is found in all classes of mollusks except for the bivalves.
The first bona fide radula dates to the Early Cambrian,[3] although trace fossils from the earlier Ediacaran have been suggested to have been made by the radula of the organism Kimberella.[WP]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
A specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart[GO]. structure of dense connective tissue in the heart that separates the atria from the ventricles. It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support.
A nerve that is part of a parasympathetic nervous system [Automatically generated definition].
An endothelium that is part of a glomerular capillary.
A nerve trunk that is part of a sympathetic nervous system [Automatically generated definition].
nerve trunk of sympathetic nervous system
nerve trunk of sympathetic part of autonomic division of nervous system
A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle of lymph vessel of respiratory system
respiratory system lymphatic vessel smooth muscle
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle tissue of blood vessel of respiratory system
respiratory system blood vessel smooth muscle
In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.
A phalanx located between proximal and distal phalanges.
consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit
Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin
in some groups such as whales, there are multiple intermediate phalanges
Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)
A distal phalanx that is part of a hand digit 2 [Automatically generated definition].
A distal phalanx that is part of a hand digit 3 [Automatically generated definition].
forelimb medial ungual phalanx of artiodactyl
A distal phalanx that is part of a hand digit 4 [Automatically generated definition].
A distal phalanx that is part of a hand digit 5 [Automatically generated definition].
A distal phalanx that is part of a foot digit 1 [Automatically generated definition].
A distal phalanx that is part of a foot digit 2 [Automatically generated definition].
A distal phalanx that is part of a foot digit 3 [Automatically generated definition].
hindlimb medial ungual phalanx of artiodactyl
A distal phalanx that is part of a foot digit 4 [Automatically generated definition].
A distal phalanx that is part of a foot digit 5 [Automatically generated definition].
A middle phalanx that is part of a hand digit 2 [Automatically generated definition].
intermediate phalanx of 2nd digit of hand
A middle phalanx that is part of a hand digit 3 [Automatically generated definition].
intermediate phalanx of 3rd digit of hand
A middle phalanx that is part of a hand digit 4 [Automatically generated definition].
intermediate phalanx of 4th digit of hand
A middle phalanx that is part of a hand digit 5 [Automatically generated definition].
intermediate phalanx of 5th digit of hand
A middle phalanx that is part of a foot digit 2 [Automatically generated definition].
A middle phalanx that is part of a foot digit 3 [Automatically generated definition].
A middle phalanx that is part of a pedal digit 4 [Automatically generated definition].
A middle phalanx that is part of a pedal digit 5 [Automatically generated definition].
A proximal phalanx that is part of a hand digit 2 [Automatically generated definition].
proximal phalanx of second digit of hand
A proximal phalanx that is part of a hand digit 3 [Automatically generated definition].
A proximal phalanx that is part of a hand digit 4 [Automatically generated definition].
proximal phalanx of fourth digit of hand
A proximal phalanx that is part of a hand digit 5 [Automatically generated definition].
A proximal phalanx that is part of a pedal digit 1 [Automatically generated definition].
A proximal phalanx that is part of a pedal digit 2 [Automatically generated definition].
proximal phalanx of second digit of foot
A proximal phalanx that is part of a pedal digit 3 [Automatically generated definition].
A proximal phalanx that is part of a pedal digit 4 [Automatically generated definition].
proximal phalanx of fourth digit of foot
A proximal phalanx that is part of a pedal digit 5 [Automatically generated definition].
A distal phalanx that is part of a hand digit 1 [Automatically generated definition].
The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects.
A proximal phalanx that is part of a hand digit 1 [Automatically generated definition].
Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid
We follow http://www.ncbi.nlm.nih.gov/pubmed/11523816 (Morriss-Kay) in definingenumerating the components of the skull vault. Note that there is a conflict with Kardong; e.g. in fig 7.10, Kardong places the squamosal in the temporal series. We cannot place the vault as entirely part of the dermatocranium as it has a small splanchnocranium contribution and a sclerotomal contribution
The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium.[well established][VHOG]
Terminology notes. we include calvarium as a synonym, but Gray's Anatomy's list includes the Ethmoid and Sphenoid bone in the Calvaria. Some books (and HPO) state that calvaria consists of just the frontal bone, parietal bone, temporal bone, and occipital bone. Note vault may not be precisely equivalent to calvaria
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]
a diverticulum of the hindgut endoderm [ISBN10:0073040584 (Vertebrates, Kardong)]
part_of embryo in EHDAA2 - note differences in humans
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]
(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]
VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826
primitive streak - blastopore - germ ring
Any of the four veins in the developing vertebrate embryo which run along each side of the vertebral column
current we conflate the cardinal vein and cardinal vein system
outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition
distinction between trophectoderm and trophoblast unclear/inconsistent in many sources
The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]
(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]
BTO has this has part of the trophoblast
embryonic structures which begin as undifferentiated mesenchyme attaching to the caudal end of the gonads. The gubernaculum is present only during the development of the urinary and reproductive organs, being replaced by distinct vestiges in males and females[WP]. Enitoinguinal ligaments that, in the male, connect the fetal testis to the developing scrotum, and, in the female, connect the ovaries to the uterus[MP]
WP def is male/female, split term? EMAP is male-specific. vestigial adult in FMA. TODO
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Early outgrowth of presumptive limb.[AAO]
developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm
The embryonic structure that gives rise to the corneal ectoderm
An inguinal canal that is part of a female organism. Conveys the round ligament + the ilioinguinal nerve.[WP,unvetted].
in MP, this is implicitly part of female reproductive system, but not female genitalia
An inguinal canal that is part of a male organism. Conveys the spermatic cord and its coverings + the ilioinguinal nerve.[WP,unvetted].
in MP, this is implicitly part of male reproductive system, but not male genitalia
The footlike extension of podocytes that interdigitate with one another to form the walls of the glomerular capillaries
multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
note that media, dorsal fins etc have AERs.
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
Proliferative region that is part of the developing fin fold or fin.[TAO]
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
The head of the epididymis receives spermatozoa via the efferent ducts of the mediastinum of the testis. It is characterized histologically by a thin myoepithelium. The concentration of the sperm here is dilute
This has a thicker myoepithelium than the head region, as it is involved in absorbing fluid to make the sperm more concentrated.
The fibrous cord that connects the tip of the styloid process of the temporal bone to the lesser horn of the hyoid bone
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta
derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast.
blood vessel that is connected to the yolk sac.
layer of the endoderm of the extraembryonic tissue.
transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed).
Portion of tissue that is the innermost layer of the cornea and consists of a monolayer of ploygonal cells.[TAO]
A continuous cartilaginous formation in mesenchyme of the second pharyngeal arch in the embryo. The longer cranial or styloid segment is continuous with the otic capsule; its inferior end is angulated and is situated very close to the oropharynx. The smaller caudal segment is in contact with the body and greater horn of the hyoid cartilaginous structure
Classically defined as: a structure... develop the stapes, the styloid processes, the stylohyoid ligaments, and the lesser cornua of the hyoid bone; its proximal end gives rise to the stylohyoid ligament. Relationship to stapes disputed.
in EHDAA2 this also develops from 3rd arch Mes from NC
An nonvascular extraembryonic basement membrane that forms on the inner surface of the trophectoderm during placenta morphogenesis and is secreted by the distal parietal endoderm; required for the maternofetal exchange of nutrients and is important for the postgastrulation development[MP]. a thick multilayered basement membrane between the parietal endoderm cells and the trophoblast cells
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
vascular network that is connected to the yolk sac.
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
A bone that is part of a fin [Automatically generated definition].
A metaphysis that is in_distal_side_of a diaphysis.
A metaphysis that is in_proximal_side_of a diaphysis.
An epiphysis that adjacent_to a distal metaphysis.
An epiphysis that adjacent_to a proximal metaphysis.
The collection of all skeletal elements in an individual limb.
Skeletal subdivision that is part of the limb.[VSAO]
EHDAA2 considers hip and shoulder joints part of limb skeleton.
An epiphysis that is part of a humerus [Automatically generated definition].
An epiphysis that is part of a tibia [Automatically generated definition].
An epiphysis that is part of a femur [Automatically generated definition].
An epiphysis that is part of a radius [Automatically generated definition].
An epiphysis that is part of an ulna [Automatically generated definition].
An epiphysis that is part of a phalanx of a manus [Automatically generated definition].
An epiphysis that is part of a fibula [Automatically generated definition].
An epiphysis that is part of a metatarsal bone [Automatically generated definition].
An epiphysis that is part of a metacarpal bone [Automatically generated definition].
An epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition].
An epiphysis that is part of a metacarpal bone of digit 2 [Automatically generated definition].
An epiphysis that is part of a metacarpal bone of digit 3 [Automatically generated definition].
An epiphysis that is part of a metacarpal bone of digit 4 [Automatically generated definition].
An epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition].
An epiphysis that is part of a metatarsal bone of digit 2 [Automatically generated definition].
An epiphysis that is part of a metatarsal bone of digit 3 [Automatically generated definition].
An epiphysis that is part of a metatarsal bone of digit 4 [Automatically generated definition].
An epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition].
A portion of bone tissue that is part of a epiphysis [Automatically generated definition].
A portion of bone tissue that is part of a distal epiphysis [Automatically generated definition].
A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition].
A periosteum that is part of a epiphysis [Automatically generated definition].
A distal epiphysis that is part of a humerus [Automatically generated definition].
A distal epiphysis that is part of a tibia [Automatically generated definition].
A distal epiphysis that is part of a femur [Automatically generated definition].
Head of the femur that articulates with the tibia and fibula.[AAO]
A distal epiphysis that is part of a radius [Automatically generated definition].
A distal epiphysis that is part of a ulna [Automatically generated definition].
A distal epiphysis that is part of a phalanx of manus [Automatically generated definition].
A distal epiphysis that is part of a fibula [Automatically generated definition].
The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles.
A proximal epiphysis that is part of a femur [Automatically generated definition].
A proximal epiphysis that is part of a radius [Automatically generated definition].
A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition].
A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition].
A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition].
A proximal epiphysis that is part of a manual digit 1 phalanx [Automatically generated definition].
proximal epiphysis of phalanx of manual digit 1
proximal epiphysis of phalanx of manual digit I
A proximal epiphysis that is part of a manual digit 2 phalanx [Automatically generated definition].
basal epiphysis of phalanx of index finger
proximal epiphysis of phalanx of manual digit 2
proximal epiphysis of phalanx of manual digit II
proximal epiphysis of phalanx of index finger
A proximal epiphysis that is part of a manual digit 3 phalanx [Automatically generated definition].
basal epiphysis of phalanx of middle finger
proximal epiphysis of phalanx of manual digit 3
proximal epiphysis of phalanx of manual digit III
proximal epiphysis of phalanx of middle finger
A proximal epiphysis that is part of a manual digit 4 phalanx [Automatically generated definition].
basal epiphysis of phalanx of ring finger
proximal epiphysis of phalanx of manual digit 4
proximal epiphysis of phalanx of manual digit IV
proximal epiphysis of phalanx of ring finger
A proximal epiphysis that is part of a manual digit 5 phalanx [Automatically generated definition].
basal epiphysis of phalanx of fifth finger
basal epiphysis of phalanx of little finger
proximal epiphysis of phalanx of manual digit 5
proximal epiphysis of phalanx of manual digit V
proximal epiphysis of phalanx of little finger
A proximal epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition].
proximal epiphysis of first metacarpal bone
A proximal epiphysis that is part of a metacarpal bone of digit 2 [Automatically generated definition].
proximal epiphysis of second metacarpal bone
A proximal epiphysis that is part of a metacarpal bone of digit 3 [Automatically generated definition].
proximal epiphysis of third metacarpal bone
A proximal epiphysis that is part of a metacarpal bone of digit 4 [Automatically generated definition].
proximal epiphysis of fourth metacarpal bone
A proximal epiphysis that is part of a metacarpal bone of digit 5 [Automatically generated definition].
proximal epiphysis of fifth metacarpal bone
A proximal epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition].
proximal epiphysis of first metatarsal bone
A proximal epiphysis that is part of a metatarsal bone of digit 2 [Automatically generated definition].
proximal epiphysis of second metatarsal bone
A proximal epiphysis that is part of a metatarsal bone of digit 3 [Automatically generated definition].
proximal epiphysis of third metatarsal bone
A proximal epiphysis that is part of a metatarsal bone of digit 4 [Automatically generated definition].
proximal epiphysis of fourth metatarsal bone
A proximal epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition].
proximal epiphysis of fifth metatarsal bone
A proximal epiphysis that is part of a distal phalanx of manual digit 2 [Automatically generated definition].
basal epiphysis of distal phalanx of index finger
base of distal phalanx of second digit of hand
proximal epiphysis of distal phalanx of manual digit II
proximal epiphysis of distal phalanx of index finger
proximal epiphysis of distal phalanx of manual digit 2
A proximal epiphysis that is part of a distal phalanx of manual digit 3 [Automatically generated definition].
base of distal phalanx of third digit of hand
proximal epiphysis of distal phalanx of manual digit III
proximal epiphysis of distal phalanx of middle finger
proximal epiphysis of distal phalanx of manual digit 3
A proximal epiphysis that is part of a distal phalanx of manual digit 4 [Automatically generated definition].
basal epiphysis of distal phalanx of fourth finger
basal epiphysis of distal phalanx of ring finger
base of distal phalanx of fourth digit of hand
proximal epiphysis of distal phalanx of manual digit IV
proximal epiphysis of distal phalanx of ring finger
proximal epiphysis of distal phalanx of manual digit 4
A proximal epiphysis that is part of a distal phalanx of manual digit 5 [Automatically generated definition].
basal epiphysis of distal phalanx of fifth finger
basal epiphysis of distal phalanx of little finger
base of distal phalanx of fifth digit of hand
proximal epiphysis of distal phalanx of manual digit V
proximal epiphysis of distal phalanx of little finger
proximal epiphysis of distal phalanx of manual digit 5
A proximal epiphysis that is part of a middle phalanx of manual digit 2 [Automatically generated definition].
basal epiphysis of middle phalanx of index finger
base of middle phalanx of second digit of hand
proximal epiphysis of middle phalanx of manual digit II
proximal epiphysis of middle phalanx of index finger
proximal epiphysis of middle phalanx of manual digit 2
A proximal epiphysis that is part of a middle phalanx of manual digit 3 [Automatically generated definition].
basal epiphysis of middle phalanx of middle finger
base of middle phalanx of third digit of hand
proximal epiphysis of middle phalanx of manual digit III
proximal epiphysis of middle phalanx of middle finger
proximal epiphysis of middle phalanx of manual digit 3
A proximal epiphysis that is part of a middle phalanx of manual digit 4 [Automatically generated definition].
basal epiphysis of middle phalanx of fourth finger
basal epiphysis of middle phalanx of ring finger
base of middle phalanx of fourth digit of hand
proximal epiphysis of middle phalanx of manual digit IV
proximal epiphysis of middle phalanx of ring finger
proximal epiphysis of middle phalanx of manual digit 4
A proximal epiphysis that is part of a middle phalanx of manual digit 5 [Automatically generated definition].
basal epiphysis of middle phalanx of fifth finger
basal epiphysis of middle phalanx of little finger
base of middle phalanx of fifth digit of hand
proximal epiphysis of middle phalanx of manual digit V
proximal epiphysis of middle phalanx of little finger
proximal epiphysis of middle phalanx of manual digit 5
A proximal epiphysis that is part of a proximal phalanx of manual digit 2 [Automatically generated definition].
base of proximal phalanx of index finger
base of proximal phalanx of second digit of hand
base of proximal phalanx of second finger
proximal epiphysis of proximal phalanx of manual digit II
proximal epiphysis of proximal phalanx of index finger
proximal epiphysis of proximal phalanx of manual digit 2
A proximal epiphysis that is part of a proximal phalanx of manual digit 3 [Automatically generated definition].
basal epiphysis of proximal phalanx of middle finger
base of proximal phalanx of middle finger
base of proximal phalanx of third digit of hand
base of proximal phalanx of third finger
proximal epiphysis of proximal phalanx of manual digit III
proximal epiphysis of proximal phalanx of middle finger
proximal epiphysis of proximal phalanx of manual digit 3
A proximal epiphysis that is part of a proximal phalanx of manual digit 4 [Automatically generated definition].
basal epiphysis of proximal phalanx of fourth finger
basal epiphysis of proximal phalanx of ring finger
base of proximal phalanx of fourth digit of hand
base of proximal phalanx of fourth finger
proximal epiphysis of proximal phalanx of manual digit IV
proximal epiphysis of proximal phalanx of ring finger
proximal epiphysis of proximal phalanx of manual digit 4
A proximal epiphysis that is part of a proximal phalanx of manual digit 5 [Automatically generated definition].
basal epiphysis of proximal phalanx of little finger
base of proximal phalanx of fifth digit of hand
base of proximal phalanx of fifth finger
base of proximal phalanx of little finger
proximal epiphysis of proximal phalanx of manual digit V
proximal epiphysis of proximal phalanx of little finger
proximal epiphysis of proximal phalanx of manual digit 5
A proximal epiphysis that is part of a distal phalanx of manual digit 1 [Automatically generated definition].
proximal epiphysis of distal phalanx of manual digit I
proximal epiphysis of distal phalanx of thumb
proximal epiphysis of distal phalanx of manual digit 1
A proximal epiphysis that is part of a proximal phalanx of manual digit 1 [Automatically generated definition].
basal epiphysis of proximal phalanx of thumb
proximal epiphysis of proximal phalanx of manual digit I
proximal epiphysis of proximal phalanx of thumb
proximal epiphysis of proximal phalanx of manual digit 1
An epiphysis that is part of a phalanx [Automatically generated definition].
A proximal epiphysis that is part of a phalanx [Automatically generated definition].
A distal epiphysis that is part of a phalanx [Automatically generated definition].
One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain.
Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO]
Either of two veins (left gastric and right gastric) that drain blood away from the stomach and lesser curvature.
A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra.
In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar)
it's not clear if the XAO class belongs here or below
A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also include the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted]
A metapodium region that is part of a manus.
Note that along with FMA we treat this as a limb segment rather than a purely skeletal element
Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
mesopodial segment of the pes, including the tarsal skeleton and associated tissues.
this term refers to the limb segment. See also: tarsal bones and tarsal skeleton
MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin).
Sum of all sensory systems in an organism.
in MA this groups pericardium, pleura and periotoneal cavity lining
this class may be merged into 'serous sac'
Any collection of muscles that is part of a head [Automatically generated definition].
Any collection of muscles that is part of a body wall [Automatically generated definition].
define generically to encompass both vertebrates and invertebrates
Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition].
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here
Any collection of muscles that is part of a neck [Automatically generated definition].
Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition].
see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)
the collection of muscles that acts on the pharynx.
Any collection of muscles that is part of a vertebral column [Automatically generated definition].
Any collection of muscles that is part of a back [Automatically generated definition].
Any collection of muscles that is part of a pelvic girdle [Automatically generated definition].
A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles.
Any collection of muscles that is part of a chest [Automatically generated definition].
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
Any collection of muscles that is part of an arm [Automatically generated definition].
Any collection of muscles that is part of a hip [Automatically generated definition].
Any collection of muscles that is part of a shoulder [Automatically generated definition].
Any collection of muscles that is part of a tongue [Automatically generated definition].
Any collection of muscles that is part of a larynx [Automatically generated definition].
Any collection of muscles that is part of a trunk [Automatically generated definition].
Any collection of muscles that is part of a limb [Automatically generated definition].
Any collection of muscles that is part of a forelimb [Automatically generated definition].
Any collection of muscles that is part of a hindlimb [Automatically generated definition].
Any collection of muscles that is part of a perineum [Automatically generated definition].
Any collection of muscles that is part of a lower arm [Automatically generated definition].
Any collection of muscles that is part of a foot [Automatically generated definition].
Any collection of muscles that is part of a manus [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.
A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition].
interatrial septum cardiac muscle tissue
cardiac muscle tissue of interatrial septum
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
A portion of cardiac muscle tissue that is part of a papillary muscle [Automatically generated definition].
cardiac muscle tissue of papillary muscle
A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a iliacus [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a gluteus maximus [Automatically generated definition].
skeletal muscle tissue of gluteus maximus
A portion of skeletal muscle tissue that is part of a quadriceps femoris [Automatically generated definition].
skeletal muscle tissue of quadriceps femoris
A portion of skeletal muscle tissue that is part of a tibialis anterior [Automatically generated definition].
skeletal muscle tissue of tibialis anterior
A portion of skeletal muscle tissue that is part of a deltoid [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a teres major [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a biceps brachii [Automatically generated definition].
skeletal muscle tissue of biceps brachii
A portion of skeletal muscle tissue that is part of a digastric [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a mylohyoid [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a orbicularis oculi [Automatically generated definition].
skeletal muscle tissue of orbicularis oculi
A portion of skeletal muscle tissue that is part of a masseter [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a temporalis [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a levator palpebrae superioris [Automatically generated definition].
skeletal muscle tissue of levator palpebrae superioris
A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a pectoralis major [Automatically generated definition].
skeletal muscle tissue of pectoralis major
A portion of skeletal muscle tissue that is part of a rectus abdominis [Automatically generated definition].
skeletal muscle tissue of rectus abdominis
A portion of skeletal muscle tissue that is part of a supraspinatus [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a internal intercostal muscle [Automatically generated definition].
skeletal muscle tissue of internal intercostal muscle
A portion of skeletal muscle tissue that is part of a transversus thoracis [Automatically generated definition].
skeletal muscle tissue of transversus thoracis
A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition].
smooth muscle tissue of lobular bronchiole
A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition].
smooth muscle tissue of terminal bronchiole
A portion of smooth muscle tissue that is part of a respiratory bronchiole [Automatically generated definition].
smooth muscle tissue of respiratory bronchiole
A muscle that is attached to a vertebra of the vertebral column.
A muscle organ that is part of a anal part of perineum.
A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition].
A vasculature that is part of a muscle organ [Automatically generated definition].
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
A papillary muscle that is part of a right ventricle [Automatically generated definition].
A papillary muscle that is part of a left ventricle [Automatically generated definition].
A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of trabecula carnea of right ventricle
A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
cardiac muscle tissue of trabecula carnea of left ventricle
thickened ridge of bone that contains the tooth sockets on bones that bear teeth.
In humans, the tooth-bearing bones are the maxilla and the mandible. The mineral content of alveolar bone is mostly hydroxyapatite, which is also found in enamel as the main inorganic substance
The alveolar part of mandible is the part of the mandible, adjacent to the teeth, containing the dental alveolus. [WP,unvetted].
A projection or outgrowth of tissue from a larger body or organ.
should be declared sijoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]
Anatomical projection that is composed of bone tissue.
A testis that is in the left side of the genitalia [Automatically generated definition].
A testis that is in the right side of the genitalia [Automatically generated definition].
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.
A vascular network consisting of blood vessels.
A kidney that is part of a left side of organism [Automatically generated definition].
A kidney that is part of a right side of organism [Automatically generated definition].
the MA term, even though plural, represents the singular, as it is an isa child of artery. We use the FMA set term as it is the closest match, but the semantics of set terms are unclear
the layer of secretory cells which lines the epididymis
External capsule is an organ subdivision of the telencephalon which is made up primarily of myelinated axonal neural tissue (white matter). The external capsule is a sheet-like fiber bundle located lateral to the to the putamen and globus pallidus which projects dorsally to the white matter underlying the cerebral cortex[FMA].
A zone of the ethmoid that is received into the ethmoidal notch of the frontal bone and roofs in the nasal cavities. [WP,modified].
The layer of uterine endometrium overlying the implanted chorionic vesicle and facing the uterine cavity
An eye that is part of a left side of organism [Automatically generated definition].
An eye that is part of a right side of organism [Automatically generated definition].
the thick circular layer of smooth gastric musculature encircling the gastroesophageal junction that functions to reduce backflow into the esophagus from the stomach
TODO - split? check FMA:63048 ! circular muscle layer of abdominal part of esophagus
this class was made obsolete, as uberon does not include 'Set of X' classes. For now, the FMA class for set of plantar digital arteries proper is under UBERON:0004540, but it is unclear if this is correct
obsolete set of proper plantar digital arteries
An artery that is part of a digit [Automatically generated definition].
check part_of - do we need term for digit + metacarpal/tarsal bones?
A digital artery that is part of a forelimb [Automatically generated definition].
A digital artery that is part of a hindlimb [Automatically generated definition].
Any vein containing deoxygenated blood that is located in a finger or toe.
A digital vein that is part of a forelimb.
A digital vein that is part of a hindlimb [Automatically generated definition].
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all arteries.
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
The part of the venous system that drains the general body tissues[Kardong]
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
elements are to be defined spatially/topologically
The tenth rib has only a single articular facet on its head. [WP,unvetted].
May sometimes be a floating rib in humans
The eleventh rib has a single articular facet on the head, which is of rather large size. It has no necks or tubercles, and is pointed at its anterior ends. The eleventh has a slight angle and a shallow costal groove. [WP,unvetted].
In humans: The twelfth rib has a single articular facet on the head, which is of rather large size. It has no necks or tubercles, and is pointed at its anterior ends. The twelfth has angle nor costal groove; it is much shorter than the eleventh rib, and its head is inclined slightly downward. Sometimes the twelfth rib is even shorter than the first rib. [WP,unvetted].
under discussion: whether to generalize this beyond mammals, making it purely order-defined
elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae
third cervical vertebra of axial skeleton
The capsule surrounding the inner ear mechanism.
developmental relationships need to be checked
Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO]
The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG]
relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO]
relationship loss: part_of otic and occipital (AAO:0000993)[AAO]
Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG]
in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
the blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism
the blood vessels that convey blood from the glomerulocapillary network to the capillary bed of the proximal convoluted tubule
arteriola glomerularis efferens capsulae renalis
the connective tissue that surrounds the spleen
An ependyma that is part of a third ventricle [Automatically generated definition].
An ependyma that is part of a lateral ventricle [Automatically generated definition].
An ependyma that is part of a fourth ventricle [Automatically generated definition].
The epithelial lining of the luminal space of the urinary bladder.
transitional epithelium of urinary bladder
The infraorbital artery is an artery in the head that runs in the maxilla, emerging through the infraorbital foramen, just under the orbit of the eye. [WP,unvetted].
the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein
should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]
A muscularis mucosa that is part of a esophagus.
lamina muscularis of esophageal mucous membrane
the process projecting downward from either side of the sphenoid bone, in vertebrates divided into two plates, an inner and an outer (sometimes called the lateral and medial); the posterior nares pass through the space, called the pterygoid fossa, between the processes
TODO - check AAO:0000521-pterygoid and MA:0001471-pterygoid bone. MA also has 'inner plate of pterygoid process' as a syn for MA:0001471, FMA has lateral/medial plates. Seems likely inner = lateral (see MP:0004452).
Process that projects from posterior margin of commissure into subocular space.[AAO]
relationship loss: part_of anterior quadratocranial commissure (AAO:0010061)[AAO]
processus pterygoideus ossis sphenoidalis
A keratinized stratified squamous epithelium that is part of a tongue.
the triangular ridge on the dorsal aspect of the scapula which separates the supra- from the infraspinatous fossa and where the trapezius and deltoid muscles are attached
the cleithrum, the major shoulder bone of extinct land vertebrate ancestors,.. appears to survive as the scapular spine in living mammals[Matsuoka, PMC1352163]
The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces.
The temporal process of the zygomatic bone, directed backward and medialward, is concave, presenting medially a rough, triangular area, for articulation with the maxilla, and laterally a smooth, concave surface, the upper part of which forms the anterior boundary of the temporal fossa, the lower a part of the infratemporal fossa. Near the center of this surface is the zygomaticotemporal foramen for the transmission of the zygomaticotemporal nerve.
The zygomatic process of the temporal bone is a long, arched process projecting from the lower part of the squamous portion of the temporal bone. It articulates with the zygomatic bone. This process is at first directed lateralward, its two surfaces looking upward and downward; it then appears as if twisted inward upon itself, and runs forward, its surfaces now looking medialward and lateralward.
A dorsal process on the lower jaw associated with muscle attachment. It may be formed by a separate coronoid bone or as a process of the dentary. In most living (and many extinct) mammals, the most dorsal of the three proximal processes of the jaw.
TAO:0001673 coronoid process, a bony projection on dentary
two broad plates directed dorsomedially from the pedicles; these fuse at the dorsal midline, and complete the dorsal wall of the vertebral foramen
Paired plates that form the neural arch. The lateral margin of each lamina rests dorsal to the superior end of the pedicel, and the medial end fuses to the medial end of the opposite lamina.[AAO]
An anatomical wall that is part of an aorta, enclosing the luminal space.
the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers
A muscular coat that is part of a seminal vesicle [Automatically generated definition].
The membranous portion of the wall between the two lower chambers of the heart
The membranous septum is the upper part of ventricular septum[GO:0003149].
membranous part of interventricular septum
membranous portion of interventricular septum
pars membranacea (septi interventricularis)
The muscular portion of the wall between the two lower chambers of the heart
The muscular septum is the lower part of the ventricular septum[GO]
muscular part of interventricular septum
pars muscularis (septi interventricularis)
One of: the 4th ventricle median or lateral apertures.
The thin epithelium-like membrane composed of ependymal cells that lines the ventricular system of the brain and the spinal cord.
unlike other epithelia, there is no basement membrane under the ependymal epithelium[ISBN-10:0387949542]
FMA breaks ependyma into ependyma proper (a subdivsion of epithelium) and epithelium of choroid plexus
Part of the lateral ventricle that extends posteriorly into the occipital lobe.
A nerve root that extends_fibers_into a trigeminal nerve.
A nerve root that extends_fibers_into a facial nerve.
A nerve root that extends_fibers_into a hypoglossal nerve.
A triangular field that is a lateralward projection of the postero-lateral part of the anterior column[WP, modified by cjm].
TODO - check relationship to spinal cord lateral column. in FMA funiculus=white and horn=grep
the band of grey substance spanning the midline of the spinal cord that surrounds the central canal
commissura grisea anaterior medullae spinalis
commissura grisea posterior medulla spinalis
apex cornu posterioris medullae spinalis
apex of dorsal gray column of spinal cord
The molecular layer of the dentate gyrus that is bounded by the pial surface superficially and the dentate gyrus granule cell layer deep. It is divided into 2 or more sublayers.
Part of fornix adjacent to the crura where they join together at the midline underneath the corpus callosum
The columns (anterior pillars; fornicolumns) of the fornix arch downward in front of the interventricular foramen and behind the anterior commissure, and each descends through the gray substance in the lateral wall of the third ventricle to the base of the brain, where it ends in the corpus mammillare. [WP,unvetted][Wikipedia:Columns_of_fornix].
The sensory system for the sense of balance.
The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system].
FMA and NIF have no part information for this class. This is a GAT in FMA
Fan shaped white matter mass comprised of afferent and efferent fibers from the cerebral cortex arranged in radially arrayed bundles, converging towards the internal capsule (Carpenter, Core Text of Neuroanatomy, 3rd ed, 1985, pg. 30; Heimer, The Human Brain and Spinal Cord, 2nd ed., 1995, pg 84).
A transitional zone between the presubiculum and the entorhinal area in the mouse (Paxinos-2001), the rat (Swanson-1998) and the primate (Zilles-1990). Defined on the basis of cytoarchitecture, it is more similar to the presubiculum than to the entorhinal area (Zilles-1990). (from Brain Info)
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane.
we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
The term "middle temporal visual area" was first used by Allman and Kaas (1971) for a region of the owl monkey brain located on the "caudal third of the middle temporal gyrus." Functionally, it contains "a complete representation of the contralateral half of the visual field... This representation of the visual field (MT) corresponds to a histologically distinct area adjacent and rostral to area 19... The horizontal meridian divides MT into a lateral portion representing the upper visual quadrant and a medial portion representing the lower quadrant. The center of gaze is represented in the caudal portion of MT bordering area 19."
peritoneum connecting the greater curvature of stomach with the hilum of the spleen[umich]. part of the greater omentum; derived from the dorsal mesogastrium in the embryo.
Mesenteric fold extending from the greater curvature of the stomach to the spleen. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
in MA, EMAPA and EHDAA2 this is part of the dorsal mesogastrium. In wikipedia, and the above source, it is derived from the DM. This is a generic ligament in MA, we infer this and assert that this is a nonskeletal ligament
peritoneum that attaches the spleen to the posterior abdominal wall over the left kidney. develops from the dorsal mesogastrium of the embryo[umich]
ligamentum splenorenale (lienorenale, phrenicosplenicum)
Multiple sources support greater omentum assignment. E.g. http://medical-dictionary.thefreedictionary.com/splenorenal+ligament. We change the MA part_of assignment to develops_from
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
A vein running parallel to the superior and inferior pancreatico-duodenal arteries that drains blood from the pancreas and duodenum into the superior mesenteric or portal veins.
Superior posterior pancreaticoduodenal vein
vena pancreaticoduodenalis superior posterior
A clear, viscous secretion that helps to lubricate the urethra for spermatozoa to pass through, neutralizing traces of acidic urine in the urethra, and helps flush out any residual urine or foreign matter. It is possible for this fluid to pick up sperm, remaining in the urethral bulb from previous ejaculations, and carry them out prior to the next ejaculation[WP].
An epithelium that is part of a naris [Automatically generated definition].
the specialized epithelium of the Peyer's patch
An epithelium that is part of a Harderian gland [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
Area of the Peyer's patch where B cells proliferate and differentiate into plasma cells
An endothelium that is part of a vena cava [Automatically generated definition].
An endothelium that is part of a outflow tract [Automatically generated definition].
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
An endothelium that is part of an arterial system [Automatically generated definition].
An endothelium that is part of a venous system [Automatically generated definition].
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
respiratory system blood vessel endothelium
TODO. http://www.ncbi.nlm.nih.gov/pubmed/8167659
Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO]
General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here
An opening in the skull or other bones[WP].
TODO check fenestra vs fossa. fenestra = hole, fossa = depression with bottom?
a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches
TODO - check relationship to bulbus arteriosus
A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities.
Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)
An appendage that is part of a appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues.
While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
One of the columns of erectile tissue forming the dorsum and sides of the penis.
A triangular double membrane, consisting of glial cells and fibers (Heimer, 1996) separating the anterior horns of the lateral ventricles of the brain. It is situated in the median plane and bounded by the corpus callosum and the body and columns of the fornix.
septum pellucidum of telencephalic ventricle
The ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised.
anulus fibrosus (diskus intervertebralis)
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
Brodmann area 29, also known as granular retrolimbic area 29 or granular retrosplenial cortex, is a cytoarchitecturally defined portion of the retrosplenial region of the cerebral cortex. In the human it is a narrow band located in the isthmus of cingulate gyrus. Cytoarchitecturally it is bounded internally by the ectosplenial area 26 and externally by the agranular retrolimbic area 30 (Brodmann-1909).
A cytoarchitecturally defined portion of the retrosplenial region of the cerebral cortex. In the human it is a narrow band located in the isthmus of cingulate gyrus. Cytoarchitecturally it is bounded internally by the ectosplenial area 26 and externally by the agranular retrolimbic area 30[BTO:0003978].
In the human this area is called ectosplenial area 26. It is a cytoarchitecturally defined portion of the retrosplenial region of the cerebral cortex. It is a narrow band located in the isthmus of cingulate gyrus adjacent to the fasciolar gyrus internally. It is bounded externally by the granular retrolimbic area 29[BTO:0003979].
Any of the veins that parallel the arcuate arteries, receive blood from the interlobular veins and straight venules, and terminate in the interlobar veins.
A subregion of the cerebellar cortex, consisting of the most medial zone of the cerebellar cortex, stradding the midline. May be continuous with the lateral cerebellar hemispheres in some areas of the cerebellum, e.g., dorsally, or separated by deeper fissures in others (e.g., ventrally)
In bony fish, or teleosts, it has been proposed that the cerebellar auricles, which receive a large amount of input from the vestibulolateral line system, constitute the vestibulocerebellum and are homologues of the flocculonodular lobe of higher vertebrates along with the corpus cerebelli, which receives spinocerebellar and tectocerebellar fibers. The labyrinth and the lateral line organs of lampreys have structural and functional similarity. An important difference between the two structures is that the arrangement of the lateral line organs are such that they are sensitive to relative motion of the fluid surrounding the animal, whereas the labyrinths, having very similar sensing mechanisms, are sensitive to endolymph, providing information concerning the animal's own equilibrium of the body and orientation in space
The crista ampullaris is the sensory organ of rotation located in the semicircular canal of the inner ear. The function of the crista ampullaris is to sense angular acceleration and deceleration.
The deep cervical lymph nodes are a group of cervical lymph nodes found near the internal jugular vein. They can be divided into upper and lower groups, or superior and inferior groups. Alternatively, they can be divided into deep anterior cervical lymph nodes and deep lateral cervical lymph nodes. They can also be divided into three groups: superior deep jugular, middle deep jugular, and 'inferior deep jugular'.
The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule.
The medial palpebral ligament (tendo oculi), about 4 mm. in length and 2 mm. in breadth, is attached to the frontal process of the maxilla in front of the lacrimal groove. Crossing the lacrimal sac, it divides into two parts, upper and lower, each attached to the medial end of the corresponding tarsus. As the ligament crosses the lacrimal sac, a strong aponeurotic is given off from its posterior surface; this expands over the sac, and is attached to the posterior lacrimal crest.
the subdivision of the laminated olfactory cortex with only three main layers that receive monosynaptic input from the olfactory bulb via the lateral olfactory tract; it is located bilaterally in the ventrolateral forebrain and is commonly divided into anterior and posterior regions
Piriform cortical regions are present in the brains of amphibians, reptiles and mammals. The piriform cortex is among three areas that emerge in the telencephalon of amphibians, situated caudally to a dorsal area, which is caudal to a hippocampal area. Farther along the phylogenic timeline, the telencephalic bulb of reptiles as viewed in a cross section of the transverse plane extends with the archipallial hippocampus folding toward the midline and down as the dorsal area begins to form a recognizable cortex. As mammalian cerebrums developed, volume of the dorsal cortex increased in slightly greater proportion, as compared proportionally with increased overall brain volume, until it enveloped the hippocampal regions. Recognized as neopallium or neocortex, enlarged dorsal areas envelop the paleopallial piriform cortex in humans and Old World monkeys. Among taxonomic groupings of mammals, the piriform cortex and the olfactory bulb become proportionally smaller in the brains of phylogenically younger species. The piriform cortex occupies a greater proportion of the overall brain and of the telencephalic brains of insectivores than in primates. The piriform cortex continues to occupy a consistent albeit small and declining proportion of the increasingly large telencephalon in the most recent primate species while the volume of the olfactory bulb becomes less in proportion
In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle.
TODO - is this a vein or set of veins? in MA it is a venous blood vessel
A nerve in the head that carries signals from the cochlea of the inner ear to the brain. It is part of the vestibulocochlear nerve, the 8th cranial nerve which is found in higher vertebrates; the other portion of the 8th cranial nerve is the vestibular nerve which carries spatial orientation information from the semicircular canals. The cochlear nerve is a sensory nerve, one which conducts to the brain information about the environment, in this case acoustic energy impinging on the tympanic membrane. The cochlear nerve arises from within the cochlea and extends to the brainstem, where its fibers make contact with the cochlear nucleus, the next stage of neural processing in the auditory system[WP].
vestibulocochlear VIII nerve cochlear component
vestibulocochlear nerve cochlear component
Amphibian larvae, sometimes called pollywogs or tadpoles, hatch from eggs and begin to grow limbs and other adult physical features at various times, depending on the species, before they metamorphose into the adult form.
Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
This begins with the newly hatched first-instar larva, through its maturation to the end of the last larval stage. An example of this process is found in Drosophila melanogaster.
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
An organ segment that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
The cavity of a gastrula forming a primitive gut.
The primitive gut that forms during gastrulation in the developing blastula. It develops into the digestive tract of an animal. As primary mesenchyme cells detach from the vegetal pole in the blastula and enter the fluid filled cavity in the center (the blastocoel), the remaining cells at the vegetal pole flatten to form a vegetal plate. This buckles inwards towards the blastocoel in a process called invagination. The cells continue to be rearranged until the shallow dip formed by invagination transforms into a deeper, narrower pouch formed by the gastrula's endoderm. This narrowing and lengthening of the archenteron is driven by convergent extension. The open end of the archenteron is called the blastopore. The filopodia--thin fibers formed by the mesenchyme cells--found in a late gastrula contract to drag the tip of the archenteron across the blastocoel. The endoderm of the archenteron will fuse with the ectoderm of the blastocoel wall. At this point gastrulation is complete, and the gastrula has a functional digestive tube. The indentation that is actually formed is called the lip of the blastopore in amphibians and fish, and the primitive streak in birds and mammals. Each is controlled by the dorsal blastopore, and primitive node (also known as Hensen's node), respectively
glomerulus of the mature vertebrate kidney, or metanephros.
A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition].
juxtaglomerular apparatus of the mature vertebrate kidney, or metanephros.
juxtaglomerular apparatus of metanephros
The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment.
a glomus differs from a glomerulus in that each vascular glomus services several tubules
Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO]
The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG]
GO treats glomus and pronephric glomerulus differently
A basibranchial element that is bone. Basibranchial elements are ventral, median, and associated with a single pharyngeal arch in the pharyngeal arch 3-7 skeleton
Medial element to which other parts of the hyoid apparatus are attached.[AAO]
Replacement bone that is ventral, median, and associated with a single pharyngeal arch in the pharyngeal arch 3-7 skeleton.[TAO]
relationship loss: develops_from copula (TAO:0001220)[TAO]
relationship loss: part_of hyoid apparatus skeleton (AAO:0000682)[AAO]
relationship loss: subclass basibranchial element (TAO:0001914)[TAO]
Dermal bone on the margin of the scapula. The cleithrum is attached to the skull in fishes, but free from the latter in amphibians and disappears early in the evolution of reptiles.
Dermal bone that articulates dorsally with the supracleithrum and ventro-medially with the scapula and coracoid and mesocoracoid bone when the last bone is present. With the posttemporal and supracleithrum, the cleithrum supports the primary pectoral girdle. The cleithrum is located immediately behind the branchial cavity.[TAO]
Paired bones of intramembranous origin. Each cleithrum extends medially from a point near the suprascapular-scapular articulation to invest the anterior margin of the suprascapula, and occasionoally it may extend to the dorsal (medial) surface. Usually, this bone is bifurcate.[AAO]
relationship loss: part_of scapular area (AAO:0000935)[AAO]
Commonly, the cleithrum is a large, well-ossified bone provided with a dorsal and a ventral arm that form an angle of about 90 or a few more degrees. The dorsal arm may end in a sharp or spine-like process to articulate with the supracleithrum. At the confluence of both arms the bone presents a blade extending postero-ventrally and that may have different development among fishes. The anterior edge of the cleithrum is usually thick and may produce a medial plate of different degrees of development.[TAO]
Found in some early members of Chelonia (e.g. Triassochelys), but missing in all later forms.
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]
Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]
relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]
Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]
In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
Endochondral bone that is paired and forms part of the socket for the humerus in tetrapods and acts as base of the pectoral fin in fish.
Endochondral bone that articulates dorsally with the scapula and with the mesocoracoid when the latter is present, posteriorly with the lower two or three proximal radials and antero-ventrally with the cleithrum. The coracoid develops from the scapulo-coracoid cartilage. The coracoid is paired.[TAO]
Paired cartilaginous structures or endochondral bones located on the posterolateral portions of the zonal area of the pectoral girdle.[AAO]
The coracoid is a triangular shaped-bone that usually has an anteriorly directed long process that may joins its counterpart in some fish groups. It may be perforated by the coracoid foramen or it may be notched dorsally and forms the scapulo-coracoid foramen together with a similar notch of the ventral margin of the scapula.[TAO]
In Theria, coracoid bones non-existent or fused with the shoulder blades to form coracoid processes[WP]. Procoracoid+coracoid are homologuous with coracoid of teleostomi. The coracoid is a triangular shaped-bone that usually has an anteriorly directed long process that may joins its counterpart in some fish groups. It may be perforated by the coracoid foramen or it may be notched dorsally and forms the scapulo-coracoid foramen together with a similar notch of the ventral margin of the scapula
see discussion in Kardong - suggests using procoracoid (anterior coracoid) for the element in birds, reptiles, amphibians and fish, and reserving coracoid for the new synapsid/therian structure.
Dermal and endochondral compound bone that results from the fusion of the dermal angular and the endochondral articular and forms the posterior part of the lower jaw. It articulates with the dentary anteriorly and with the retroarticular postero-medially. The anguloarticular is paired.[TAO]
Endochondral ossification of the posterior articular part of Meckel's cartilage.[AAO]
relationship loss: develops_from articular bone (TAO:0001805)[TAO]
The presence of an anguloarticular is interpreted as a synapomorphy of the Clupeocephala (Patterson and Rosen, 1977; Arratia, 1999).[TAO]
TAO has a distinct class for articular - in fact we need (at least) 3 classes here - articular, anguloarticular and malleus, arranged into a single VHOG group
A tooth- or denticle-covered plate which is attached to the sphenoid stem[Palaeos].
Azygous, dermal bone of intramembranous origin that underlies the ventral surface of the braincase in anurans and salamanders. In caecilians, the parasphenoid and other bones are fused to form the Os basale.[AAO]
Dermal bone that forms part of the base of the skull and the lateral walls of the braincase through its ascending processes. It may articulate with the vomer anteriorly, the prootics and exoccipitals laterally, and the basioccipital posteriorly. The parasphenoid is an elongate median bone.[TAO]
relationship loss: overlaps parasphenoid-pterosphenoid joint (TAO:0002217)[TAO]
Paired, endochondral bones forming the anterior, and lateral walls of the otic capsules.
Endochondral bone that sutures with the pterosphenoid anteriorly, the sphenotic and pterotic dorsally, the parasphenoid ventrally, the basioccipital postero-ventrally, the exoccipital posteriorly, and occasionally, with the intercalar posteriorly. The dorsal edge of the prootic contributes to the hyomandibular facet. The prootic bears foramina that accommodate branches of the trigeminal and facial nerves. The prootic is a paired bone.[TAO]
relationship loss: develops_from basal plate cartilage (TAO:0001425)[TAO]
relationship loss: overlaps prootic-pterosphenoid joint (TAO:0002033)[TAO]
Endochondral bone that is located at the dorsal part of the occipital region of the cranium or the dorso-posterior part of the skull[TAP,modified].
Endochondral bone that is located at the dorsal part of the occipital region of the cranium or the dorso-posterior part of the skull. It forms the dorsal margin of the foramen magnum. Commonly the supraoccipital articulates with the parietals anteriorly, the epiotics laterally, and the exoccipitals posteroventrally. The supraoccipital is an unpaired median bone.[TAO]
The supraoccipital ties the occiput to the dermal skull table.[Palaeos]
a bone on the dorsal side of the great foramen of the skull, usually forming a part of the occipital in the adult, but distinct in the young..[TFD]
relationship loss: overlaps supraoccipital-parietal joint (TAO:0005264)[TAO]
See Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution, Fourth Edition (2006) McGraw-Hill, p.237 Table 7.1; usually forming a part of the occipital in the adult, but distinct in the young
Sliver of bone that invest part of or all the posterior aspect of each antorbital plane.[AAO]
The cartilaginous autopalatine forms from the anterior palatoquadrate arch. The first sign of ossification is visible at the anterior tip where it articulates with the maxilla (7.6 mm). In adults there are three processes at the anterior portion of the palatine: a ventromedial process, which forms the socket of the small ball- and- socket joint with the preethmoid; a dorsomedial process, which is connected by a short ligament to the ethmoid; and a lateral process, which extends toward the first infraorbital. Possession of a dorsomedial process, which abuts the ethmoid, is a unique feature shared by Cypriniformes (Fink and Fink, 1981). The palatine has two components, the autopalatine (derived from pars autopalatine) and the dermal component having teeth, the dermopalatine Arratia & Schultze 1990. The element in cypriniforms is only the cartilage part, so that it is more correct to name it autopalatine and not as palatine in general that it implies a fusion of elements (as in perciforms).[ZFA]
A small, circular, white spot (approximately 2-3 mm across) on the surface of the yellow yolk of an egg that has been laid. The nucleus of the egg is in the germinal disc.
A layer of cells formed at one pole of macrolecithal eggs such as the yolky egg of birds. The yolk prevents the division from taking place through the egg, resulting in meroblastic cleavage during the many cleavage divisions. At the animal pole (containing less yolk than the vegetal pole), the zygote divides and subdivides, forming the blastoderm, which gradually spreads around the yolk and forms the embryo. The blastoderm is composed of two layers, the epiblast and the hypoblast, which enclose the fluid-filled blastocoel cavity.
Paired element that articulates anterioly with the basihyal and posteriorly with the ceratohyal hypohyals.[AAO]
Replacement bone that is bilaterally paired and articulates with the anterior ceratohyal posteriorly.[TAO]
The dorsal component of the mandibular arch
Column of catilage, remnant in the adult of the larval palatoquadrate cartilage, that is located lateral or antero-lateral to the auditory capsule.[AAO]
Skeletal element that consists of the scapula and the coracoid[VSAO, modified].
todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present
Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO]
Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO]
either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos]
ZFA defines as precursor to scapula and coracoid. Cartilage in TAO
In the fetal heart, the foramen ovale (also ostium secundum of Born or falx septi) allows blood to enter the left atrium from the right atrium. It is one of two fetal cardiac shunts, the other being the ductus arteriosus (which allows blood that still escapes to the right ventricle to bypass the pulmonary circulation). Another similar adaptation in the fetus is the ductus venosus. In most individuals, the foramen ovale (pronounced /fɒˈreɪmən oʊˈvɑːli/) closes at birth. It later forms the fossa ovalis[WP].
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
dermis-derived entity that is made of skeletal tissue.
An evagination of the terminal portion of the intestine of Elasmobranchii. Function formerly thought to be related to digestion or excretion, but now considered to secrete high concentrations of excess sodium chloride. Found also in the coelacanth Latimeria chalumnae[BTO].
does not include FMA:15724 Rectal gland // epithelial tissue gland - concentrates & secretes excess Na & Cl in sharks. large shark liver produces copious amounts of urea, making the shark hyperosmotic to seawater, & thus a shark acts like a fresh water fish, constantly gaining water. Excess salts are concentrated by the rectal gland and secreted
An organ for excreting excess salts. It is found in elasmobranchs, seabirds, and some reptiles.[WP].
In sharks, salt glands are found in the rectum, but in birds and reptiles, they are found in or on the skull, in the area of the eyes, nostrils or mouth. In crocodiles, the salt is excreted through the tongue. Such glands work by active transport via sodium-potassium pump that moves salt from the blood into the gland, where it can be excreted as a concentrated solution. Salt glands function to keep salt balance, and allow marine vertebrates to drink seawater
A salt gland located in the cranium or cranial region.
A gland that is part of an anal canal [Automatically generated definition].
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
cartiligionous skeletal structure of skull
Replacement bone tissue that forms within cartilage[VSAO, modified].
the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
TODO - add more general class for other kinds of mineralized tissue
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Tooth that is attached to the vomer.[TAO]
relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO]
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular
Do not manually classify under here - bones are automatically classified
Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified].
Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA].
The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, http://en.wikipedia.org/wiki/Diaphysis].
Anatomical system that consists of all the joints of the body.
Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP].
One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Opening between the nasal cavity and the nasopharynx.[AAO]
The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]
Fish don't have choanae, instead they have two pairs of external nostrils
In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity.
The tarsi (tarsal plates) are two comparatively thick, elongated plates of dense connective tissue, about 2.5 cm. in length; one is found in each eyelid, and contributes to its form and support. They directly abut the lid margins.
In most taxa (birds, mammals, lizards), the tarsal plate is described as a dense, fibrous connective tissue, possibly including cartilage, present within one or both of the upper and lower eyelids (Gau- thier et al., 1988; Rieppel, 2000). In humans, the tarsal plate of the upper eyelid is composed of collagens types I, III, and V, as well as glycosaminogly- cans (chondroitin sulphate 4 and 6), aggrecan, and cartilage oligomeric matrix proteins but lacks collagen type II as well as chondrocytes (Milz et al., 2005). Thus, for humans, the upper tarsal plate represents neither a truly fibrous nor a truly cartilagi- nous element but instead one that is composed of a unique transitional tissue (Milz et al., 2005). In many birds, lizards, and Sphenodon (the tuatara), the upper eyelid has lim- ited mobility and a putative tarsal plate is instead found within the lower eyelid (Underwood, 1970; Gau- thier et al., 1988).
An eyelid tarsus that is part of a upper eyelid [Automatically generated definition].
An eyelid tarsus that is part of a lower eyelid [Automatically generated definition].
A vasa recta that is part of a outer medulla of kidney [Automatically generated definition].
outer zone of medulla of kidney vasa recta
vasa recta of outer zone of medulla of kidney
vasa recta of outer zone of renal medulla
A vasa recta that is part of a inner medulla of kidney [Automatically generated definition].
inner zone of medulla of kidney vasa recta
set of inner region of renal pyramids vasa recta
vasa recta of inner zone of medulla of kidney
vasa recta of inner zone of renal medulla
vasa recta of set of inner region of renal pyramids
A submucosa that is part of a respiratory system [Automatically generated definition].
A submucosa that is part of a larynx [Automatically generated definition].
A lamina propria that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lamina propria mucosa
lamina propria mucosa of apparatus respiratorius
lamina propria mucosa of respiratory system
lamina propria of apparatus respiratorius
respiratory system lamina propria mucosa
A lamina propria that is part of a gastrointestinal system.
A lamina propria that is part of a gallbladder [Automatically generated definition].
A serous membrane that is part of a digestive system [Automatically generated definition].
serous membrane of gastrointestinal system
A serous membrane that is part of a gallbladder [Automatically generated definition].
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
anatomical wall of lower chamber of heart
the mucous membrane lining the respiratory tract
TODO - split respiratory tract mucosa from respiratory system mucosa
mucosa of organ of apparatus respiratorius
mucous membrane of apparatus respiratorius
A mucosa that is part of a gastrointestinal system.
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
An urothelium that is part of a urethra [Automatically generated definition].
the epithelial lining of the luminal space of the kidney pelvis
transitional epithelium of kidney pelvis
A mucous gland that is part of a larynx [Automatically generated definition].
A mucous gland that is part of the skin.
the thymic connective tissue which extends into the parenchyma
A secretion that is part of a endocrine pancreas [Automatically generated definition].
A secretion that is part of a exocrine pancreas [Automatically generated definition].
A secretion that is part of a esophagus [Automatically generated definition].
A secretion that is part of a pancreas [Automatically generated definition].
A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20–30% of the volume of the semen along with spermatozoa and seminal vesicle fluid
Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline.
An organ component layer that is part of a blood vessel.
A basal lamina that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius basal lamina of connective tissue
basal lamina of connective tissue of apparatus respiratorius
basal lamina of connective tissue of respiratory system
respiratory system basal lamina of connective tissue
A basal lamina that is part of a respiratory airway [Automatically generated definition].
basal lamina of connective tissue of respiratory airway
A basal lamina that is part of a bronchus [Automatically generated definition].
basal lamina of connective tissue of bronchi
basal lamina of connective tissue of bronchial trunk
basal lamina of connective tissue of bronchus
bronchi basal lamina of connective tissue
bronchial trunk basal lamina of connective tissue
bronchus basal lamina of connective tissue
An epithelium that is part of a uterine cervix [Automatically generated definition].
The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium
the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
An epithelium that is part of a penis [Automatically generated definition].
An epithelium that is part of a oviduct [Automatically generated definition].
in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label
columnar epithelium of the Fallopian tube
An epithelium that is part of a seminal vesicle [Automatically generated definition].
An epithelium that is part of a vas deferens [Automatically generated definition].
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
An epithelium that is part of a salivary gland [Automatically generated definition].
the cellular avascular layer of the renal tubule luminar surfaces
An epithelium that is part of an endometrium [Automatically generated definition].
In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)
epithelium of tunica mucosa of endometrium
An epithelium that is part of a prepuce of penis [Automatically generated definition].
the stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule
epithelial tissue of seminiferous tubule
epithelial tissue of seminiferous tubule of testis
epithelium of seminiferous tubule of testis
An epithelium that is part of a upper respiratory tract [Automatically generated definition].
epithelial tissue of upper respiratory tract
upper respiratory tract epithelial tissue
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
lower respiratory tract epithelial tissue
An epithelium that is part of a larynx [Automatically generated definition].
composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]
An epithelium that is part of a lacrimal gland [Automatically generated definition].
An epithelium that is part of a terminal bronchus [Automatically generated definition].
the cellular avascular layer of the kidney luminar surfaces
Epithelium of the gallbladder and the intrahepatic and extrahepatic bile ducts.
The epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO].
An epithelium that is part of a extrahepatic bile duct [Automatically generated definition].
epithelial tissue of extrahepatic bile duct
extrahepatic bile duct epithelial tissue
An epithelium that is part of a intrahepatic bile duct [Automatically generated definition].
epithelial tissue of intrahepatic bile duct
intrahepatic bile duct epithelial tissue
A band of ectodermal cells growing from the epithelium of the embryonic jaws into the underlying mesenchyme and giving rise to the primordia of the enamel organs of the teeth.
In the epidermis of embryonic birds, there remains a transient thickening that is comparable to the early formation of the dental lamina in the mouse
check MA placement, this structure is the developing structure
A medulla that is part of a thyroid [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition].
A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum skeletal muscle tissue
skeletal muscle of anal part of perineum
skeletal muscle tissue of anal part of perineum
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: http://en.wikipedia.org/wiki/Lip#Muscles_acting_on_the_lips
A smooth muscle tissue that is part of a hepatic duct.
A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition].
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system endothelium of artery
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
vein endothelium of apparatus respiratorius
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
An endothelium that is part of a lymph node [Automatically generated definition].
the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall
endothelium of trunk of systemic arterial tree
trunk of systemic arterial tree endothelium
An endothelium that is part of the cardiovascular system.
A mesentery that is part of a digestive system [Automatically generated definition].
A connective tissue that surrounds a skeletal muscle tissue.
connective tissue of skeletal muscle tissue
portion of connective tissue of skeletal muscle
portion of connective tissue of skeletal muscle tissue
skeletal muscle portion of connective tissue
skeletal muscle tissue connective tissue
skeletal muscle tissue portion of connective tissue
skeletal muscle tissue textus connectivus
textus connectivus of skeletal muscle tissue
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
An alveolus that is part of a right lung [Automatically generated definition].
An alveolus that is part of a left lung [Automatically generated definition].
A sympathetic nerve trunk that is part of a thorax [Automatically generated definition].
nerve trunk of sympathetic nervous system of thorax
nerve trunk of sympathetic part of autonomic division of nervous system of thorax
sympathetic nervous system nerve trunk of thorax
thorax nerve trunk of sympathetic nervous system
thorax nerve trunk of sympathetic part of autonomic division of nervous system
thorax sympathetic nervous system nerve trunk
A vasculature that is part of a retina [Automatically generated definition].
Dermal bone that covers the otic region and may articulate with its antimere medially, with the frontal bone anteriorly, the pterotic laterally, the supraoccipital medio-posteriorly, and the epiotic and extrascapula latero-posteriorly. The parietal is a paired bone.[TAO]
relationship loss: overlaps frontal-parietal joint (TAO:0005255)[TAO]
relationship loss: overlaps inter-parietal joint (TAO:0005245)[TAO]
relationship loss: overlaps posttemporal-parietal joint (TAO:0002059)[TAO]
The parietal is a flat, commonly squarish or rectangular bone.[TAO]
Dermal bone that bears part of the supraorbital canal and usually covers a large area of the neurocranium occupying part of the ethmoidal, orbitosphenoid, and otic regions. Commonly, the frontal bone articulates with its antimere medially, with lateral ethmoid, orbitosphenoid and pterosphenoid ventrolaterally, with supraorbital bone(s), autosphenotic and pterotic laterally, and with parietal posteriorly.[TAO].
relationship loss: overlaps frontal-pterotic joint (TAO:0001711)[TAO]
relationship loss: overlaps inter-frontal joint (TAO:0001922)[TAO]
relationship loss: overlaps lateral ethmoid-frontal joint (TAO:0002032)[TAO]
relationship loss: overlaps mesethmoid-frontal joint (TAO:0001678)[TAO]
The frontal bone may be paired or unpaired. The frontal bone of actinopterygians is homologous to the parietal of tetrapods. Actinopterygians do not have a frontal bone. For details, see Schultze (2008) and Wiley (2008).[TAO]
The frontal bone in teleost fish is the homolog of the parietal bone in tetrapods
Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye.
note that the AAO and ZFA class is a cavity
A layer of tissue in the eye of many vertebrate animals, that lies immediately behind or sometimes within the retina. It reflects visible light back through the retina, increasing the light available to the photoreceptors
The tapetum lucidum is a biologic reflector system that is a common feature in the eyes of vertebrates. Typically absent in diurnal animals. In vertebrates, the tapetum lucidum exhibits diverse structure, organization and composition. The tapetum lucidum represents a remarkable example of neural cell and tissue specialization as an adaptation to a dim light environment and, despite these differences, all tapetal variants act to increase retinal sensitivity by reflecting light back through the photoreceptor layer. These variations regarding both its location and structure, as well as the choice of reflective material, may represent selective visual adaptations associated with their feeding behavior, in response to the use of specific wavelengths and amount of reflectance required.[PMID:14738502].
Two morphologic types of tapetum lucidum can be observed in the eyes of fish: one in the choroid that occurs in elasmobranchs, and the other which occurs in teleosts and lies in the pigment epithelium of the retina
It normally functions at low light levels to provide the light-sensitive retinal cells with a second opportunity for photon-photoreceptor stimulation, thereby enhancing visual sensitivity
A part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation. The parietal eye is a part of the epithalamus, which can be divided into two major parts; the epiphysis (the pineal organ, or pineal gland if mostly endocrine) and the parietal organ (often called the parietal eye, or third eye if it is photoreceptive). It arises as an anterior evagination of the pineal organ or as a separate outgrowth of the roof of the diencephalon. In some species, it protrudes through the skull.[4] The parietal eye uses a different biochemical method of detecting light than rod cells or cone cells in a normal vertebrate eye[WP].
A group of nodes lying along the external jugular vein; they drain the skin and superficial structures over the region of the sternocleidomastoid muscle and anterior cervical regions. Efferent vessels drain to the deep cervical lymph nodes. Lymph nodes can be further subdivided into anterior and lateral groupings.
Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP].
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
A portion of the urogenital ridge which is the source of much of the urinary system[WP].
part_of or develops_from urogenital ridge?
One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].
Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]
Visceral endoderm, a population of extraembyonic endoderm, is an extraembryonic tissue that functions in a regulatory capacity but does not contribute directly to the formation of any adult organs[PMID:15905405]. primitive endoderm-derived tissue which remains in contact with and surrounds the extra-embryonic ectoderm and the epiblast and provides signals for the differentiation and patterning of the epiblast; a small number of visceral endoderm cells also contribute to the endoderm of the embryonic gut[MP].
Gilbert uses visceral endoderm as a synonym for primitive endoderm/hypoblast
precursors of the anterior visceral endoderm that arises at the distal tip of the embryo[MP]
Belt-like region of presumptive mesoderm at the equator of the late blastula.
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
Thickened layer of skin surrounding fingernails and toenails. Beneath the cuticle is a thin layer of a membrane known as the pterygium. The function is to protect the area between the nail and epidermis from exposure to harmful bacteria. The vascularization pattern is similar to that of perionychium. The eponychium is the end of the proximal fold that folds back upon itself to shed an epidermal layer of skin onto the newly formed nail plate. This layer of non-living, almost invisible skin is the cuticle that 'rides out' on the surface of the nail plate. Together, the eponychium and the cuticle form a protective seal. The cuticle on the nail plate is dead cells and is often removed during manicure, but the eponychium is living cells and should not be touched.[6] The perionyx is the projecting edge of the eponychium covering the proximal strip of the lunula[WP].
The mass of tissue made up of mesenchymal cells in the lung.
The mass of tissue composed of mesenchymal cells in the lobar bronchus..
An anatomical cavity, depression or pit where structures are attached.
Galen and NCITA refer to the generic structure
A depression on the surface of the lung where the bronchus, blood vessels and nerves enter.
A lung hilus that is part of the left lung.
The part of the left lung that is not covered by pleura and through which blood vessels, bronchi, nerves and lymphatics enter and leave the lung. [TFD][VHOG]
A lung hilus that is part of the right lung.
The part of the right lung that is not covered by pleura and through which blood vessels, bronchi, nerves and lymphatics enter and leave the lung. [TFD][VHOG]
Vasculature that is composed of the tubule structures that carry blood or lymph in the lungs
A specialized lobe of the right lung that extends to the left side of the organism
In mouse this is sometimes divided into intermediate and diaphragmatic lobes
in humans, the right lung typically has 3 lobes (superior, middle, inferior). The lobar fissures are often incomplete, making a connection between two apposed lobes. Conversely, more than the expected number of lobes may be produced by new fissures e.g. the azygous lobe of the lung. The additional lobes are termed 'accessory lobes' -- http://www.gpnotebook.co.uk/simplepage.cfm?ID=1120927803
this class was obsoleted as it was generated from an incorrect inference from EMAPA
The lobar bronchus alveolar system is where molecules of oxygen and carbon dioxide are passively exchanged, by diffusion, between the gaseous environment and the blood in the lobar bronchus
A the thin septum that separates adjacent pulmonary alveoli, containing connective tissue constituents of the respiratory tissue and the capillary network of the blood supply of the lung.
Alveolar smooth muscle is a type of non-striated muscle, found within the walls of the alveolus
The right lung accessory lobe lobar bronchus is the major airway within the right lung accessory lobe that starts at the division of the bronchus on the right side and ends at the point of its own subdivision into tertiary or segmental bronchi
lobar bronchus of right lung accessory lobe
right lung accessory lobe lobar bronchus
The right lung accessory lobe lobar bronchus mesenchyme is a type of tissue made up of loosely-packed mesenchymal cells in the right lung accessory lobe lobar bronchus
right lung accessory lobe lobar bronchus mesenchyme
obsolete right lung caudal lobe lobar bronchus mesenchyme
The right lung cranial lobe lobar bronchus mesenchyme is a type of tissue made up of loosely-packed mesenchymal cells in the right lung cranial lobe lobar bronchus
right lung cranial lobe lobar bronchus mesenchyme
The right lung middle lobe lobar bronchus mesenchyme is a type of tissue made up of loosely-packed mesenchymal cells in the right lung middle lobe lobar bronchus
right lung middle lobe lobar bronchus mesenchyme
The right lung lobar bronchus mesenchyme is a type of tissue made up of loosely-packed mesenchymal cells in the right lung lobar bronchus
The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra
we follow EHDAA2 in dividing the UGS into epithelium and lumen
A branch point connecting the respiratory bronchioles to the alveolar ducts[MP].
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila
for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
neuron projection bundle connecting eye with brain
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].
MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct.
Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO]
One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct.
muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP].
A sphincter muscle that is part of a anal region.
A sphincter muscle surrounding the urethra.
A urethral sphincter muscle which constricts the internal urethral orifice. It is the junction of the urethra with the urinary bladder. The muscle is made of smooth muscle, so therefore it is under involuntary control. It is kept tonically contracted by the sympathetic nervous system and during micturition, is relaxed via the parasympathetic nervous system. This is the primary muscle for preventing the release of urine[WP].
musculus sphincter urethrae membranaceae
A mesoderm that is part of a gonad [Automatically generated definition].
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A mitotically active layer of cells surrounding the brain ventricles in the adult that consists of migrating neuroblasts, astrocytes and transitory amplifying progenitor cells[MP].
A paired brain structure situated throughout the lateral walls of the lateral ventricles. It has been associated with having four distinct layers of variable thickness and cell density, as well as cellular composition[WP][Wikipedia:Subventricular_zone].
The subventricular zone (SVZ) is a paired brain structure situated throughout the lateral walls of the lateral ventricles. Along with the subgranular zone of dentate gyrus, subventricular zone serves as a source of neural stem cells in the process of adult neurogenesis. It harbors the largest population of proliferating cells in the adult brain of rodents, monkeys and humans. Neurons generated in SVZ travel to the olfactory bulb via the rostral migratory stream[BTO:0003090].
The subventricular zone (SVZ) is one of two sources of adult-born neurons in the mammalian brain, the other being the subgranular zone (SGZ) of the hippocampus. In most adult mammals, the SVZ is a three-layered sheath that lies along the lateral wall of the lateral ventricle and consists of type A, B, and C cells. Type A rest along the ventricle wall and are neuronal precursor cells, Type B are adjacent astrocytes, and Type C are immature precursors to the Type A neuroblasts. The neuronal precursor cells travel along the rostral migratory stream ensheathed in a tube of Type B astrocytes, until they reach the olfactory bulb. There they integrate into the existing cellular network and mature into local interneurons. While the majority become adult-born granule cells, a subset become periglomerular cells. Interestingly, the human SVZ differs from other mammals' in several ways. It consists of four layers rather than three: ependymal cells (layer I), a hypo cellular gap (layer II), a ribbon of astrocytes (layer III), and a transitional zone (layer IV). The astrocytes are capable of differentiating into many kinds of tissue including new neurons. However, there is no evidence that the proliferating neurons travel along the rostral migratory stream in a chain to populate the olfactory bulb with new interneurons, as is the case for other mammals[NIFSTD:nlx_144262].
Organ component which is a part of a wall of an organ.
The tissue underlying the tunica mucosa of the pharynx.
A submucosa that is part of a hypopharynx [Automatically generated definition].
tela submucosa (pars laryngea pharyngis)
A submucosa that is part of a cystic duct [Automatically generated definition].
A submucosa that is part of a cecum [Automatically generated definition].
A submucosa that is part of an appendix [Automatically generated definition].
A submucosa that is part of an ascending colon [Automatically generated definition].
A submucosa that is part of a transverse colon [Automatically generated definition].
A submucosa that is part of a descending colon [Automatically generated definition].
A submucosa that is part of a sigmoid colon [Automatically generated definition].
A submucosa that is part of a fundus of stomach [Automatically generated definition].
fundus gastricus (ventricularis) submucosa
submucosa of fundus gastricus (ventricularis)
A submucosa that is part of a body of stomach [Automatically generated definition].
corpus gastricum (ventriculare) submucosa
submucosa of corpus gastricum (ventriculare)
A submucosa that is part of a cardia of stomach [Automatically generated definition].
A submucosa that is part of a pyloric antrum [Automatically generated definition].
A submucosa that is part of a pylorus [Automatically generated definition].
A submucosa that is part of a biliary tree [Automatically generated definition].
A submucosa that is part of a common bile duct [Automatically generated definition].
submucosa of ductus choledochus (biliaris)
A submucosa that is part of a common hepatic duct [Automatically generated definition].
A submucosa that is part of a right hepatic duct [Automatically generated definition].
A submucosa that is part of a left hepatic duct [Automatically generated definition].
The submucous layer of the wall of the urinary bladder.
A submucosa that is part of a trigone of urinary bladder [Automatically generated definition].
A submucosa that is part of a neck of urinary bladder [Automatically generated definition].
A submucosa that is part of a ileum [Automatically generated definition].
A submucosa that is part of a right main bronchus [Automatically generated definition].
A submucosa that is part of a left main bronchus [Automatically generated definition].
A submucosa that is part of a main bronchus [Automatically generated definition].
A submucosa that is part of a lobar bronchus [Automatically generated definition].
A submucosa that is part of a segmental bronchus [Automatically generated definition].
A submucosa that is part of a bronchiole [Automatically generated definition].
A mucosa that is part of a ureter [Automatically generated definition].
A mucosa that is part of a epiglottis [Automatically generated definition].
A mucosa that is part of a vagina [Automatically generated definition].
A mucosa that is part of a seminal vesicle [Automatically generated definition].
A mucosa that is part of a ejaculatory duct [Automatically generated definition].
A mucosa that is part of a vas deferens [Automatically generated definition].
A mucosa that is part of a hypopharynx [Automatically generated definition].
A mucosa that is part of a cystic duct [Automatically generated definition].
A mucosa that is part of an appendix [Automatically generated definition].
A mucosa that is part of an ascending colon [Automatically generated definition].
A mucosa that is part of a transverse colon [Automatically generated definition].
A mucosa that is part of a descending colon [Automatically generated definition].
A mucosa that is part of a sigmoid colon [Automatically generated definition].
A mucosa that is part of a fundus of stomach [Automatically generated definition].
fundus gastricus (ventricularis) mucosa of organ
fundus gastricus (ventricularis) mucous membrane
fundus gastricus (ventricularis) organ mucosa
mucosa of fundus gastricus (ventricularis)
mucosa of organ of fundus gastricus (ventricularis)
mucous membrane of fundus gastricus (ventricularis)
organ mucosa of fundus gastricus (ventricularis)
A mucosa that is part of a body of stomach [Automatically generated definition].
corpus gastricum (ventriculare) mucosa of organ
corpus gastricum (ventriculare) mucous membrane
corpus gastricum (ventriculare) organ mucosa
mucosa of corpus gastricum (ventriculare)
mucosa of organ of corpus gastricum (ventriculare)
mucous membrane of corpus gastricum (ventriculare)
organ mucosa of corpus gastricum (ventriculare)
A mucosa that is part of a cardia of stomach [Automatically generated definition].
mucosa of organ of cardial part of stomach
mucosa of organ of pars cardiaca (gaster)
mucosa of organ of stomach cardiac region
mucous membrane of cardial part of stomach
mucous membrane of pars cardiaca (gaster)
mucous membrane of stomach cardiac region
A mucosa that is part of a pyloric antrum [Automatically generated definition].
mucosa of organ of stomach pyloric antrum
mucous membrane of stomach pyloric antrum
A mucosa that is part of a pylorus [Automatically generated definition].
mucosa of organ of pyloric part of stomach
mucosa of organ of stomach pyloric region
mucous membrane of pyloric part of stomach
mucous membrane of stomach pyloric region
A mucosa that is part of a biliary tree [Automatically generated definition].
A mucosa that is part of a common bile duct [Automatically generated definition].
ductus choledochus (biliaris) mucosa of organ
ductus choledochus (biliaris) mucous membrane
ductus choledochus (biliaris) organ mucosa
mucosa of organ of ductus choledochus (biliaris)
mucous membrane of ductus choledochus (biliaris)
organ mucosa of ductus choledochus (biliaris)
A mucosa that is part of a common hepatic duct [Automatically generated definition].
A mucosa that is part of a right hepatic duct [Automatically generated definition].
A mucosa that is part of a left hepatic duct [Automatically generated definition].
A mucosa that is part of a right ureter [Automatically generated definition].
A mucosa that is part of a left ureter [Automatically generated definition].
A mucosa that is part of a renal pelvis [Automatically generated definition].
A mucosa that is part of a major calyx [Automatically generated definition].
A mucosa that is part of a minor calyx [Automatically generated definition].
A mucosa that is part of a trigone of urinary bladder [Automatically generated definition].
mucosa of organ of trigone of urinary bladder
mucosa of organ of urinary bladder trigone
mucous membrane of trigone of urinary bladder
mucous membrane of urinary bladder trigone
organ mucosa of trigone of urinary bladder
trigone of urinary bladder mucosa of organ
trigone of urinary bladder mucous membrane
A mucosa that is part of a neck of urinary bladder [Automatically generated definition].
mucosa of organ of neck of urinary bladder
mucous membrane of neck of urinary bladder
A mucosa that is part of a right uterine tube [Automatically generated definition].
A mucosa that is part of a left uterine tube [Automatically generated definition].
A mucosa that is part of a male urethra [Automatically generated definition].
A mucosa that is part of a female urethra [Automatically generated definition].
A mucosa that is part of a prostatic urethra [Automatically generated definition].
mucosa of organ of prostatic part of urethra
mucous membrane of prostatic part of urethra
organ mucosa of prostatic part of urethra
prostatic part of urethra mucosa of organ
prostatic part of urethra mucous membrane
A mucosa that is part of a membranous urethra [Automatically generated definition].
intermediate part of urethra mucosa of organ
intermediate part of urethra mucous membrane
intermediate part of urethra organ mucosa
membranous part of urethra mucosa of organ
membranous part of urethra mucous membrane
mucosa of organ of intermediate part of urethra
mucosa of organ of membranous part of urethra
mucosa of organ of pars membranacea (urethrae)
mucous membrane of intermediate part of urethra
mucous membrane of membranous part of urethra
mucous membrane of pars membranacea (urethrae)
organ mucosa of intermediate part of urethra
organ mucosa of membranous part of urethra
organ mucosa of pars membranacea (urethrae)
pars membranacea (urethrae) mucosa of organ
pars membranacea (urethrae) mucous membrane
pars membranacea (urethrae) organ mucosa
A mucosa that is part of a lacrimal sac [Automatically generated definition].
A mucosa that is part of a nasal septum [Automatically generated definition].
A mucosa that is part of a palate [Automatically generated definition].
A mucosa that is part of a tongue [Automatically generated definition].
A mucosa that is part of a sphenoidal sinus [Automatically generated definition].
decide whether cavities can be part of mucosae
A mucosa that is part of a nasopharynx [Automatically generated definition].
mucosa of organ of nasal part of pharynx
mucous membrane of nasal part of pharynx
A mucosa that is part of a oropharynx [Automatically generated definition].
A mucosa that is part of a soft palate [Automatically generated definition].
A mucosa that is part of a uvula [Automatically generated definition].
A mucosa that is part of a middle ear [Automatically generated definition].
A mucosa that is part of a frontal sinus [Automatically generated definition].
A mucosa that is part of a maxillary sinus [Automatically generated definition].
A mucosa that is part of a lacrimal canaliculus [Automatically generated definition].
A mucosa that adjacent_to a paranasal sinus.
A mucosa that is part of a upper lip [Automatically generated definition].
A mucosa that is part of a lower lip [Automatically generated definition].
A mucosa that is part of a gallbladder [Automatically generated definition].
A mucosa that is part of a right main bronchus [Automatically generated definition].
mucosa of organ of right principal bronchus
mucous membrane of right principal bronchus
organ mucosa of right principal bronchus
right principal bronchus mucosa of organ
right principal bronchus mucous membrane
A mucosa that is part of a left main bronchus [Automatically generated definition].
mucosa of organ of left principal bronchus
mucous membrane of left principal bronchus
A mucosa that is part of a main bronchus [Automatically generated definition].
A mucosa that is part of a lobar bronchus [Automatically generated definition].
A mucosa that is part of a segmental bronchus [Automatically generated definition].
A mucosa that is part of a bronchiole [Automatically generated definition].
A mucosa that is part of a terminal bronchiole [Automatically generated definition].
mucosa of organ of bronchiolus terminalis
mucous membrane of bronchiolus terminalis
A mucosa that is part of a respiratory bronchiole [Automatically generated definition].
bronchiolus respiratorius mucosa of organ
bronchiolus respiratorius mucous membrane
mucosa of organ of bronchiolus respiratorius
mucosa of organ of respiratory bronchiole
mucous membrane of bronchiolus respiratorius
mucous membrane of respiratory bronchiole
organ mucosa of bronchiolus respiratorius
A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane
tympanic membrane external middle ear cavity epithelial component
inner epithelial layer of tympanic membrane
A mucosa that is part of a nasolacrimal duct [Automatically generated definition].
A mucosa that is part of a pharyngotympanic tube [Automatically generated definition].
mucosa of organ of internal auditory tube
mucosa of organ of pharyngotympanic tube
mucous membrane of internal auditory tube
mucous membrane of pharyngotympanic tube
mucuous membrane of pharyngotympanic tube
A mucosa that is part of a ethmoid sinus [Automatically generated definition].
A mucosa that is part of a hard palate [Automatically generated definition].
A mucosa that is part of a vocal cord [Automatically generated definition].
A mucosa that is part of a fallopian tube [Automatically generated definition].
A mucosa that is part of a uterine tube infundibulum [Automatically generated definition].
mucosa of infundibulum of fallopian tube
mucosa of organ of uterine tube infundibulum
mucous membrane of uterine tube infundibulum
organ mucosa of uterine tube infundibulum
uterine tube infundibulum mucosa of organ
uterine tube infundibulum mucous membrane
papillary process of caudate lobe of liver
The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP]
The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus.
currently restricted to Aves, but may be found outside - e.g. Pangolins
BTO also includes: A thickened part of the alimentary canal in some animals (as an insect or an earthworm) that is similar in function to the crop of a bird. However, we are refering to the Aves structure here.
A cluster of ➞neurons that is the most prominent longitudinally extending condensed part of a ➞nervous system.
The dorsal tubular cord of nervous tissue above the notochord of a chordate that comprises or develops into the central nervous system[BTO]. The nerve cord of chordates develops dorsally in the body as a hollow tube above the notochord. In most species it differentiates in embryogeny into the brain anteriorly and spinal cord that runs through the trunk and tail. Together the brain and spinal cord are the central nervous system to which peripheral sensory and motor nerves connect[TOL]. The dorsal nerve cord is one of the embryonic features unique to chordates, along with a notochord, a post-anal tail and pharyngeal slits. The dorsal nerve cord is a hollow cord dorsal to the notochord. It is formed from a part of the ectoderm that rolls, forming the hollow tube, compared to other animal phyla, which have solid, ventral tubes. The dorsal nerve cord is later modified into the brain and spinal cord. Dorsal nerve cord is mainly found in phylum Vertebrata[WP].
An organ part that is part of a long bone [Automatically generated definition].
An external genitalia that is part of a female reproductive system [Automatically generated definition].
in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]
external genitalia of female reproductive system
An organ that is part of a immune system [Automatically generated definition].
A gland that is part of a hemolymphoid system [Automatically generated definition].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
Amphid sensory organs are the sensory organs of nematodes[GO].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
The median hinge point extends for the entire length of the neural tube, and the lateral hinge points do not form in the spinal cord region of the neural tube[GO].
The neuropore at the anterior (rostral) end of the neural tube.
Anterior site of neural tube closure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.378, see_Kardong_KV][VHOG]
The neuropore at the posterior (caudal) end of the neural tube.
Posterior site of neural tube closure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.378, see_Kardong_KV][VHOG]
obsolete preganglionic parasympathetic nervous system
obsolete postganglionic parasympathetic nervous system
An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain.
The boundary between the diencephalon and the mesencephalon.[TAO]
relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO]
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
A temporary opening leading from the central canal of the embryonic neural tube to the exterior.
The anterior-most (rostral) portion of the wall of the neural tube, formed by closure of the anterior neuropore; the median strip of the anterior wall of the prosencephalon, which persists in a relatively unchanged state as the cerebral hemispheres grow out forward beyond the original anterior end of the prosencephalon.
A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO].
The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].
The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].
A circular ingrowth of the epidermis around the region of the mammary sprout[GO].
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous.
An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO].
An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO].
Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]
In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs.
A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO].
An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]
A simple mucus-secreting structure that is positioned at the front of the embryo, attaches the newly hatched embryo to a support before the hatchling can swim well or feed, and marks the anterior-most dorsal ectoderm[XAO].
A simple mucus-secreting structure that is positioned at the front of the embryo, attaches the newly hatched embryo to a support before the hatchling can swim well or feed, and marks the anterior-most dorsal ectoderm.[AAO]
The avian beak is an external anatomical structure, in the head region, that is adapted for feeding self and young, catching prey, probing, etc. It encompasses, but is not restricted to, the maxilla, mandible, maxillary ramaphotheca, mandibular ramaphotheca, nostril, nasal fossa, nasal bones, egg tooth and rictus[GO]. The beak, bill or rostrum is an external anatomical structure of birds which is used for eating and for grooming, manipulating objects, killing prey, probing for food, courtship and feeding young. .
The term beak is also used to refer to a similar mouthpart in some Ornithischian dinosaurs, monotremes, cephalopods, cetaceans, pufferfishes, turtles, Anuran tadpoles and sirens
class added for consistency with GO - consider merging with kidney mesenchyme.
The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO].
thin descending limb of the loop of henle
The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO].
The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology[GO].
The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla[GO].
The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive[GO].
The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO].
An epithelium that is part of a mesonephros [Automatically generated definition].
A metanephric tubule is an epithelial tube that is part of the metanephros[GO].
The metanephric cap is formed by the condensation of metanephric mesenchymal cells surrounding the ureteric bud tip[GO]. Mesenchyme closely apposed to the tips of the buds is called cap mesenchyme; it will later go on to form nephrons etc[GUDMAP].
An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO].
Any smooth muscle tissue that is part of a metanephros.
A metanephric nephron is the functional unit of the metanephros[GO].
The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]
Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO].
The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent[GO].
The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO].
It extends to the tip of the metanephric loop of Henle[GO].
The metanephric distal convoluted tubule is a portion of the metanephric nephron tubule that connects the metanephric loop of Henle to the collecting duct[GO].
The metanephric early distal convoluted tubule contains metanephric DCT cells and is vasopressin-insensitive[GO].
metanephric early distal convoluted tubule
The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus[GO].
The metanephric late distal convoluted tubule contains metanephric DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO].
metanephric late distal convoluted tubule
The metanephric long descending thin limb bend is a part of the descending thin limb of a long nephron that lies beyond the prebend segment in the metanephros[GO].
metanephric long descending thin limb bend
The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus[GO].
The metanephric prebend segment is a part of the metanephric descending thin limb that lies before the bend and exhibits permeabilities characteristic of the ascending limb, especially negligible water permeability[GO].
The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule[GO].
The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule[GO].
TODO - place mammalian xrefs here rather than at parent
The S1 portion is the initial portion of the metanephric proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO].
At the macula densa, the thick ascending limb connects to the distal convoluted tubule[GO].
The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO].
The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros[GO].
Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla in the metanephros[GO].
The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO].
The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO].
A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO].
The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO].
The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO].
Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb[GO].
The metanephric short descending thin limb is the descending thin limb of a short nephron in the metanephros that has a squamous epithelial morphology[GO].
This process pertains to the initial formation of a structure from unspecified parts[GO].
The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO].
A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO].
The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO].
The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO].
The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros[GO].
The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology[GO].
A bud is a protrusion that forms from an epithelial sheet by localized folding.
A cord of epithelial cells without a lumen and usually several cells thick.
An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.
An anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
A parenchyma that is part of a central nervous system [Automatically generated definition].
The anterior or ventral portion of the medulla oblongata is named the pyramid and lies between the anterior median fissure and the antero-lateral sulcus. Its upper end is slightly constricted, and between it and the pons the fibers of the abducent nerve emerge; a little below the pons it becomes enlarged and prominent, and finally tapers into the anterior funiculus of the medulla spinalis, with which, at first sight, it appears to be directly continuous[WP].
A remnant structure from earlier development or evolution.
Pelvic spurs are the externally visible portion of the vestigial remnants of legs found on each side of the vent in primitive snakes, such as boas and pythons. The remnants of a pelvis and femur, which have no connection with the spine, simply 'float' in the muscle mass. The femur protrudes from the snake's body and is covered by a corneal spur, which resembles a claw. Males' spurs are generally longer and more pointed than females', and are used for clasping and tickling during courtship and mating, as well as combat with other males in some species
this class refers to the external portion and its corneal covering rather than the combined pelvis plus femur.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP].
TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule
The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx.
Any of the veins that parallel the interlobular arteries, receiving blood from the peritubular capillary plexus and empty into the arcuate veins
connective tissue between the cellular elements of a structure.
A layer of the ovarian follicle that consists of granulosa cells.
At one part of the mature follicle the cells of the membrana granulosa are collected into a mass which projects into the cavity of the follicle. This is termed the discus proligerus. [Wikipedia:Membrana_granulosa, http://en.wikipedia.org/wiki/Membrana_granulosa]
granulosa cell layer of ovarian follicle
The hepatic duct is the duct that leads from the liver to the bile duct[GO]. A duct that carries bile from the liver to the small intestine[ZFA].
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same
A duct that carries bile from the liver to the small intestine.[TAO]
The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
An organ that is part of a chest [Automatically generated definition].
some sources treat the dental organ as epithelium - we treat it as the mereological sum of dentail epithelium plus dental papilla (consistent with treatment in many AOs), but this may be
A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO]
revised.Development notes: NOT develeops_from NC[UBERONREF:0000002]. Alternate definitioon: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla. Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A collecting duct of renal tubule that is part of a renal medulla [Automatically generated definition].
A collecting duct of renal tubule that is part of a outer medulla of kidney [Automatically generated definition].
A collecting duct of renal tubule that is part of a inner medulla of kidney [Automatically generated definition].
An artery that is part of a uterine cervix [Automatically generated definition].
An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP].
One of: anterior or posterior ethmoidal arteries.
A vein that is part of a thorax [Automatically generated definition].
A vein that is part of a vas deferens [Automatically generated definition].
A germinal center that is part of the spleen. The spleen germinal center is located in a secondary B follicle in the white pulp of the spleen.
A mammary gland that is part of a cervical region.
A lactiferous gland that is located in the thoracic region/breast.
Most primates have one pair of mammary glands, which are thoracic.
was obsolete as it was defined incorrectly. See Fig97 of The Anatomy of the Laboratory Mouse. May be included in future versions of this ontology that include more detailed relationships and comparisons of the arterial system
A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition].
TODO - unify terminology - check DST = TAL? Note EMAPA class appears to refer to this segment
A gland that is part of a submucosa of trachea [Automatically generated definition].
A gland that is part of a larynx submucosa [Automatically generated definition].
A stroma that is part of a choroid plexus [Automatically generated definition].
A capsule that is part of a tonsil [Automatically generated definition].
A valve that is part of a right atrium [Automatically generated definition].
tissue surrounding the loop of Henle in the renal medulla.
It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct.
The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS..
A portion of interstitial tissue that is part of a outer medulla of kidney [Automatically generated definition].
A portion of interstitial tissue that is part of a inner medulla of kidney [Automatically generated definition].
The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.
See https://sourceforge.net/p/geneontology/ontology-requests/10941/
The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment.
The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue.
An external ectoderm that is part of a optic eminence [Automatically generated definition].
A subarachnoid space that is part of a midbrain [Automatically generated definition].
Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG]
A subarachnoid space that is part of a diencephalon [Automatically generated definition].
Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG]
A subarachnoid space that is part of a hindbrain [Automatically generated definition].
Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG]
A parenchyma that is part of a head of pancreas [Automatically generated definition].
A parenchyma that is part of a right lobe of liver [Automatically generated definition].
A parenchyma that is part of a left lobe of liver [Automatically generated definition].
A parenchyma that is part of a body of pancreas [Automatically generated definition].
A parenchyma that is part of a tail of pancreas [Automatically generated definition].
An epithelium that is part of a hindlimb stylopod [Automatically generated definition].
An epithelium that is part of a toe [Automatically generated definition].
An epithelium that is part of a finger [Automatically generated definition].
An epithelium that is part of a forelimb stylopod [Automatically generated definition].
An epithelium that is part of a lower leg [Automatically generated definition].
obsoleted due to confusion between ocular fundus and other types of fundus
An ectoderm that is part of a medial nasal prominence [Automatically generated definition].
An ectoderm that is part of a optic eminence [Automatically generated definition].
A small, oval, bony chamber of the labyrinth. The vestibule contains the utricle and saccule, organs which are part of the balancing apparatus of the ear.
The vestibule is the central part of the osseous labyrinth, and is situated medial to the tympanic cavity, behind the cochlea, and in front of the semicircular canals. [http://en.wikipedia.org/wiki/Vestibule_of_the_ear][VHOG]
The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
The ventral half of the developing neural tube that is the medulla oblongata. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
A forelimb that is part of an apical ectodermal ridge [Automatically generated definition].
obsolete apical ectodermal ridge forelimb
A hindlimb that is part of an apical ectodermal ridge [Automatically generated definition].
obsolete apical ectodermal ridge hindlimb
An endocardium that is part of a interventricular septum [Automatically generated definition].
interventricular septum endocardial tissue
lobar bronchus of right lung cranial lobe
A lobar bronchus that is part of a lower lobe of right lung [Automatically generated definition].
lobar bronchus of right lung caudal lobe
A myocardium that is part of a bulbus cordis [Automatically generated definition].
A renal pelvis that is part of a metanephros.
The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG]
An anatomical cavity that is part of a yolk sac [Automatically generated definition].
In mammals, the yolk sac cavity contains fluid rather than platelets
in EHDAA2, there are separate primary and secondary yolk sac cavities
An anatomical cavity that is part of a lesser sac [Automatically generated definition].
cavity of omental bursa viewed anatomically
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition].
Mesenchyme that is part of a developing toe [Automatically generated definition].
Mesenchyme that is part of a developing trunk.
Mesenchyme that is part of a developing finger [Automatically generated definition].
In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation
Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition].
Mesenchyme that is part of a developing lower leg [Automatically generated definition].
A cardiac jelly that is part of an atrium [Automatically generated definition].
Cardiac jelly that is part of the atrium. [Bgee_curator][VHOG]
A cardiac jelly that is part of a ventricle [Automatically generated definition].
Cardiac jelly that is part of the ventricle. [Bgee_curator][VHOG]
A cardiac jelly that is part of a outflow tract [Automatically generated definition].
Cardiac jelly that is part of the outflow tract. [Bgee_curator][VHOG]
A collecting duct of renal tubule that is part of a cortex of kidney [Automatically generated definition].
An artery that supplies the renal cortex.
Artery that receives blood from the renal cortex[MP, modified]
A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells.
In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5′-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c.
The part of the renal cortex nearest to the medulla.
the tiny blood vessels that receive blood from the efferent arterioles of the glomerulus, and interact with superficial cortical nephrons allowing reabsorption and secretion between blood and the inner lumen of the nephron; peritubular capillaries are situated around the tubule and are at low pressure
Region of skin beneath the nail plate[WP].
A dorsal skin of digit that is part of a manual digit.
this class is explicitly the union of the two FMA classes
subdivision of skin of dorsal part of finger
A dorsal skin of digit that is part of a pedal digit.
subdivision of skin of dorsal part of toe
A nail bed that is part of a manual digit.
A nail bed that is part of a pedal digit.
A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP].
TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity'
ventricular system of central nervous system
A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm].
Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447].
Vascularized tela choroidea is choroid plexus.
Note that the structure in ZFA may be different
Tela choroidea that lines the tectal ventricle.
Tela chorioidea that lines the tectal ventricle.[TAO]
tela choroidea of midbrain cerebral aqueduct
Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP].
Tela chorioidea that lines the fourth ventricle.[TAO]
Tela chorioidea that lines the third ventricle[ZFA]. The part of the choroid plexus in relation to the body of the ventricle forms the vascular fringed margin of a triangular process of pia mater, named the tela chorioidea of the third ventricle, and projects from under cover of the lateral edge of the fornix. Blood is supplied by branches from the superior cerebellar artery[WP].
Tela chorioidea that lines the third ventricle.[TAO]
Tela chorioidea that lines the telencephalic ventricle.
tela chorioidea of telencephalic ventricle
tela choroidea of telencephalic ventricle
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
A portion of tissue that is part of an embryo.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
A major subdivision of the cerebellum: anterior, posterior and flocculonodular
the elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary
TODO - check developmental relationships. merge with urogenital ridge?
in eutherians, SRY transforms the indifferent gonad into testes
Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female.
structures that develop from sex cords in the female. After further development they become the ovarian follicles.
TODO check secondary vs cortical vs ovary
The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP].
A zone of skin that is part of a clitoris [Automatically generated definition].
In female human anatomy, the clitoral hood, is a fold of skin that surrounds and protects the clitoral glans. It develops as part of the labia minora and is homologous with the foreskin (equally called prepuce) in male genitals.
FMA has FMA:27886 skin of prepuce of clitoris
One of the sebaceous glands of the corona and neck of the glans penis.
FMA:19653 was previously placed here, but ISBN10:0123813611 states that no true equivalent in humans. See also https://sourceforge.net/tracker/index.php?func=detail&aid=3588536&group_id=76834&atid=1109502
The paired, lobulated, modified sebaceous glands located on the side of the clitoris in female rodents; in contrast to the preputial glands in male rodents, clitoral glands are a minor source of olfactory stimuli contributing to sexual attractivity; unlike other sebaceous glands, they undergo progressive atrophy of the glandular portion with marked ductal ectasia as rodents age.
large, lobulated, modified sebaceous glands located on the side of the clitoris in female mice; little is known about their function and, unlike other sebaceous glands, they undergo progressive atrophy of the glandular portion with marked ductal ectasia as mice age; there is no equivalent gland in humans.
there is no true anatomical equivalent in humans
The transition between the superior hypogastric plexus and the inferior hypogastric plexus.
check plexus vs nerve. WP indicates it is a 'transition'
the gangliated plexus of unmyelinated nerve fibers that ramify the stomach and intestinal submucosa
in FMA this is part of the esophagus, duodenum and intestine; this violates part-disjointness axioms in uberon
Discrete, cystlike units of the thyroid gland that are lined with cuboidal epithelium and are filled with a colloid substance, about 30 to each lobule[BTO].
A blastema is a mass of cells capable of growth and regeneration into organs or body parts. Historically blastema have been thought to be composed of undifferentiated pluripotent cells, but recent research indicates that in some organisms blastema may retain memory of tissue origin.[1] Blastemata are typically found in the early stages of an organism's development such as in embryos, and in the regeneration of tissues, organs and bone[WP]. A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise[ZFA].
the ZFA class called 'blastema' belongs with the subclass, blastema of regenerating fin/limb
An eggshell that contains chorion. An example of this is found in Drosophila melanogaster.
The nephrostome is the opening of the pronephros into the body cavity[GO].
A pronephric nephron is the functional unit of the pronephros[GO].
The structure that is the basic functional unit of the pronephros.[AAO]
The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO].
Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]
The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO].
A primary alveolar septum is a specialized epithelium that surrounds the saccule as it forms[GO].
TODO - check UBERON:0004893 interalveolar septum
A secondary alveolar septum is a specialized epithelium that subdivides the initial saccule[GO].
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO].
The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO].
A nephron that is part of a mesonephros.
The structure that is the basic functional unit of the kidney.[AAO]
Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO].
The mesonephric macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus[GO].
The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO].
A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO]
In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG]
XAO/AAO class belongs here, as it refers to mesonephric structure
The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO].
A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO].
The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO].
A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros[GO].
The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO].
The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO].
The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO].
An outpocketing of the mammary placode that develops into the mammary gland.
produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts
A lamina propria that is part of a mucosa of oral region.
The chorioallantoic membrane is a vascular membrane found in eggs of some amniotes, such as birds and reptiles. It is formed by the fusion of the mesodermal layers of two developmental structures: the allantois and the chorion. Three different layers compose the chorioallantoic membrane; these are called the chorionic epithelium, the mesenchyme and the allantoic epithelium. Blood capillaries and sinuses are found between epithelial cells of the chorionic layer, allowing close contact (within 0.2 N<m) with air found in pores of the shell membrane of the egg. As a result, the chorioallantoic membrane allows exchange of gases, such as oxygen, to developing embryos. During embryonic development of birds, the chorioallantoic membrane also plays an essential role in bone formation by transporting calcium into the embryo from the eggshell. Chorioalloantoic membranes from developing chicken eggs are routinely used in biological and biomedical research to investigate development, angiogenesis, tumors, and to propagate and investigate viruses or helminths.
The capillary lamina of choroid or choriocapillaris is a layer of capillaries that is immediately adjacent to Bruch's membrane in the choroid.
capillary lamina of choroid or choriocapillaris
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
An outflow tract that is part of a aorta.
A fiber tracts that connect the dorsal region of the two cerebral hemispheres and span the longitudinal fissure, including the corpus callosum and hippocampal commissure[MP].
The fiber tracts that connect the ventral region of the two cerebral hemispheres and span the longitudinal fissure, including the anterior and the habenular commissures[MP].
rounded portion of the malleus that articulates with the body of the incus[MP].
The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP].
A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047]
in humans develops into cortical layers II-VI
A peritoneal diverticulum in the embryonic lower anterior abdominal wall that traverses the inguinal canal. In the male it forms the tunica vaginalis testis and normally loses its connection with the peritoneal cavity; a persistent processus vaginalis in the female is known as the canal of Nuck[MP].
processus vaginalis peritonei masculinus
This is a structure present in rodents and is not present in humans. The cerebellum hemisphere structure and lobulation is dramatically different between these species.
A lobule comprising the greater part of the hemisphere of the cerebellum; its superior and inferior surfaces are separated by the horizontal fissure into major parts known as crus I (superior semilunar lobule) and crus II (inferior semilunar lobule).
MP says not present in humans; however, we group based on synonymy from multiple sources
The anterior portion of the posteroinferior lobule of the cerebellum, the posterior portion being the semilunar lobule inferior; the two are continuous with the tuber of the vermis.
lobule VIIIB (pyramis and biventral lobule, posterior part)
posterior crescentic lobule of cerebellum
simple lobule of cerebellum [h vi and vi]
The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP].
The compartment located between the marginal zone and the red pulp harboring scattered B and T lymphocytes[MP].
The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents.
The projection extending from the base of the manubrium of the malleus which contacts the upper part of the tympanic membrane where the tympanic cavity makes a deep pocket (epitympanic pocket) surrounding the cartilaginous nodule[MP].
The narrow contracted section of the malleus located between the head and the manubrium[MP].
A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP].
A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG]
median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke’s pouch and perhaps to Hatschek 's pit (amphioxus).
EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium.
the ependymal cell layer that lines the brain ventricles
in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion
region of wall of ventricular system of neuraxis
the ependymal cell layer that lines the spinal cord
ependyma of central canal of spinal cord
The lower group of sensory neuron cell bodies associated with the glossopharyngeal nerve[MP]. It is situated in a depression in the lower border of the petrous portion of the temporal bone[WP].
We follow FMA and VHOG in making the relation subclass
ganglion inferius (nervus glossopharygeus)
ganglion inferius nervus glossopharyngei
glossopharyngeal nerve inferior ganglion
inferior ganglion of glossopharyngeal nerve
inferior glossopharyngeal ganglion of the glossopharyngeal (IX) nerve
The upper ganglion of the glossopharyngeal nerve[MP]. is situated in the upper part of the groove in which the glossopharyngeal nerve is lodged during its passage through the jugular foramen. It is very small, and is usually regarded as a detached portion of the inferior ganglion
ganglion superius (nervus glossopharyngeus)
ganglion superius nervus glossopharyngei
glossopharyngeal nerve superior ganglion
superior ganglion of glossopharyngeal nerve
superior glossopharyngeal ganglion of the glossopharyngeal (IX) nerve
the group of sensory neuron cell bodies associated with the vagus nerve
the large group of sensory neuron cell bodies, anterior to the jugular vein, associated with the vagus nerve (tenth cranial nerve)
the upper ganglion of the vagus nerve located at the jugular foramen
Olfactory apparatus on the lower surface of the frontal lobe of the brain. It consists of the olfactory bulb, tract, and trigone[BTO].
Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180].
A cytoarchitectural region of the hippocampus consisting of a composite of the two outermost layers of the hippocampus, the Stratum lacunosum-moleculare and the Stratum radiatum (Carpenter-83).
Due to its small size, it is often grouped together with stratum moleculare into a single stratum called stratum lacunosum-moleculare[WP]
The term Stratum oriens is a cytoarchitectural term denoting the layer of the hippocampus that is deep to the Stratum pyramidale hippocampi and superficial to the alveus (Stephan-75).
The layer located immediately above the pyramidal cell layer in CA2 and CA1 and superficial to the stratum lucidum in CA3. Suprapyramidal region in which CA3 to CA3 associational connections and CA3 to CA1 Schaffer collateral connections are located.
the wedge-shaped fiber bundle of white matter in the dorsomedial side of the spinal cord that is made up of the fasciculus gracilis and fasciculus cuneatus; it is part of the ascending posterior column-medial lemniscus pathway that is important for well-localized fine touch and conscious proprioception
The dorsolateral ridge of gray matter in each lateral half of the spinal cord. [TFD][VHOG]
The dorsal column is a part of the spinal cord which is responsible for transporting sensory input from the body to the cerebral cortex. This part of the spinal cord is key in perceiving fine touch, such as that used to distinguish textures, along with vibration. The dorsal column also contributes to the body's system of proprioception, used to orient the body in space and to coordinate muscle movements, given information about the body's position
the region of white matter of the spinal cord that is located between the dorsal and ventral spinal roots
TODO - check relationship between column and funiculus. Also check white vs grey matter. See ventral column. Note also ZFA term 'lateral column' is part of reticular formation
the area of white matter of the spinal cord located on either side of the ventral (anterior) medial fissure
The ventral ridge of gray matter in each half of the spinal cord. [TFD][VHOG]
in MA, this is a subclass of white matter, but in WP/Gray's, the anterior column is a synonym of the grey matter section. is this the same as funiculus? See lateral column.
Cytoarchitectural part of the olfactory bulb, lying superior to the mitral cell layer and inferior to the glomerular layer. The EPL is mostly neuropil composed almost entirely of mitral and tulfted cell dendrites and granule cell dendrites and their synaptic inputs.
olfactory bulb main external plexiform layer
external plexiform layer of the olfactory bulb
The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA].
The granule cell layer contains multiple small round neurons that lack axons. Long dendritic processes of the neurons reach the more superficial layers and inhibit mitral cells and tufted cells. Small distal processes make contacts with the exiting mitral cell axons.
accessory olfactory bulb granule cell layer
inner plexiform layer of the main olfactory bulb
internal plexiform layer of olfactory bulb
internal plexiform layer of the olfactory bulb
main olfactory bulb, inner plexiform layer
the region of mitotically active layer of cells surrounding the lateral brain ventricles that consists of migrating neuroblasts, astrocytes and transitory amplifying progenitor cells, that produce neurons that migrate to the olfactory bulb
Granule cell layer is also called the DG principal cell layer. This one of the three layers of dentate gyrus that lies deep to the molecular layer and is made of densely packed layer that is four to eight granule cells thick.
Dorsal components of the striatum comprising the caudate nucleus and the putamen, in species that have distinct nuclei; the caudoputamen in species which don't.
According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (putamen and the globus pallidus) and the caudate nucleus
It may also refer to both the basal ganglia and the internal capsule collectively.
It may also refer to the putamen and caudate collectively.
The term dorsal striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes most of the striatum ( Heimer-1995 ). The boundary between this structure and the ventral striatum is indistinct in sections stained for Nissl substance.
Regional part of telencephalon in some species, e.g., rodent, equivalent to the dorsal striatum (caudate nucleus and putamen). Unlike the dorsal striatum of primates, for example, the caudoputamen is not split into separate nuclei by the fibers of the internal capsule. Rather, the internal capsule splits into fiber bundles which course through the structure.
we do not currently place rodent-specific taxon constraints here as this would cause taxon violations. There is an argument for merging this into dorsal striatum and treating the distinction as phenotypic
In the human, histologically the caudate nucleus and putamen are identically and share a common embryological origin[ISBN10:0123813611]
An epithelium that lines the nasal cavity.
this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism
An epithelium that is part of the respiratory segment of the nasal mucosa [Automatically generated definition].
That portion of the nasal mucosa containing the sensory endings for olfaction; the organ of smell[MESH].
The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa].
One of the small globular masses of dense neuropil in the olfactory bulb, containing the first synapse in the olfactory pathway[BTO].
Multi-tissue structure part of the olfactory bulb that is roughly spheroidal and encircled by olfactory sensory neuron axons that formed an anatomically distinct stalk connected to the olfactory nerve[ZFA].
An array of photoreceptors and any supporting cells found in an eye.
transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array
The most superficial layer of the neocortex characterized by a paucity of cell bodies.
lamina molecularis isocorticis [lamina I]
Layer of neocortex lying just deep to molecular layer characterized by numerous small cell bodies.
external granular layer of isocortex [layer II]
external granule cell layer of neocortex
lamina granularis externa isocorticis [lamina ii]
external granular layer of cerebral cortex
Layer of neocortex lying deep to the external granule cell layer defined cytoarchitecturally by numerous small pyramidal neurons.
external pyramidal cell layer of neocortex
external pyramidal layer of isocortex [layer iii]
lamina pyramidalis externa isocorticis [lamina iii]
external pyramidal layer of cerebral cortex
isocortex, deep supragranular pyramidal layer
layer of medium-sized and large pyramidal cells
Layer of neocortex lying deep to the external pyramidal cell layer defined cytoarchitecturally by the presence of numerous small cells
Relatively undeveloped in some mammals such as the tenrec.
internal granular layer of isocortex [layer iv]
internal granule cell layer of neocortex
lamina granularis interna isocorticis [lamina iv]
Layer of neocortex lying deep to the internal granule cell layer (layer 4) defined cytoarchitecturally by the predominance of large pyramidal cell bodies
internal pyramidal cell layer of neocortex
internal pyramidal layer of isocortex [layer v]
lamina pyramidalis interna isocorticis [lamina v]
isocortex, infragranular pyramidal layer
Innermost layer of neocortex lying deep to the internal pyramidal cell layer defined cytoarchitecturally by cells of varying size.
lamina multiformis isocorticis [lamina vi]
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
An arachnoid mater that surrounds a brain.
A sex gland that is part of a female reproductive system.
A sex gland that is part of a male reproductive system.
An arachnoid mater that is part of a telencephalon.
A gray matter that is part of a cerebral hemisphere.
BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon
the vertical groove found on the median line of the upper lip, extending to the nose
vestigial in humans. In humans, the philtrum is formed where the nasomedial and maxillary processes meet during embryonic development (colloquially known as Hulse lines). When these processes fail to fuse fully in humans, a cleft lip (sometimes called a 'hare lip') can result. A flattened or smooth philtrum can be a symptom of fetal alcohol syndrome or Prader-Willi syndrome
A composite structure of the telencephalon that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the anterior perforated substance, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance (Heimer-1995; adapted from Brain Info).
The term ventral striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the olfactory tubercle, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance ( Heimer-1995 ).
A suture between frontal and nasal bones
articulation of the nasal bone with frontal bone
The paranephric body (or paranephric fat or pararenal fat) is collection of adipose tissue located superficial to the renal fascia. The perirenal fat, or adipose capsule of kidney, is deep to the renal fascia but superficial to the renal capsule.
The adipose capsule of kidney (or perinephric fat or perirenal fat) is a structure between the renal fascia and renal capsule, and may be regarded as a part of the latter. A different structure, the pararenal fat, is the adipose tissue superficial to the renal fascia.
the small parasympathetic ganglion found anterior to the submandibular gland that provides postsynaptic fibers to the sublingual gland
Brain region located around or in relation to the ventricular system that is highly vascularized and distinguished by the lack of a blood brain barrier.
All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330)
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla
A otic capsule endochondral element that is composed primarily of a cartilage tissue.
Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO]
In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans). todo - check EMAPA
the cartilage or bony capsule surrounding the inner ear mechanism
In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)
Groove that is in the developing ventral optic cup and through which blood vessels pass to the enclosed mesenchyme[ZFA]. a ventral fissure in the developing optic cup through which blood vessels pass to the enclosed mesenchyme[Free online medical dictionary].
A break in the continuity of the optic cup where the two sides of the cup meet.[AAO]
The folded arrangement of the vertebrate retina and RPE [retinal pigment epithelial] provides an evolutionary explanation for the occurrence of the choroid fissure, as proposed more than a century ago. Early in evolution, before the optic cup invaginated, the axons from retinal ganglion cells would simply have run over the surface of the structure. Hence, one can view the optic nerve as having acted rather like a rope in linking the retina to higher centres: the developing eye cup has simply wrapped around this 'rope', and the developing axons have thereby not needed to penetrate the retina.[well established][VHOG]
Develeopment notes: As the eye starts to develop, a gap opens on the underside of each eye bud. This gap provides a way for the developing eye to be nourished. This gap, called the optic fissure, has to close before the eye is fully developed. Coloboma is the incomplete closer of the optic fissure
This tract conveys interoceptive, proprioceptive, and exteroceptive information from the body's internal organs, and from the trunk, extremities, and neck region to the Cerebellum.
The spinocerebellar tract is a set of axonal fibers originating in the spinal cord and terminating in the ipsilateral cerebellum. This tract conveys information to the cerebellum about limb and joint position[Wikipedia:Spinocerebellar_tract].
An area of mesenchymal cells that contains signals which instruct the developing limb or fin bud to form along the anterior/posterior axis.
Morphologically indistinct signaling region found in the posterior portion of the limb bud. Associated with anterior-posterior patterning of the digits.[AAO]
Sonic hedgehog (Shh) produced by ZPA represents the key mediator of the polarizing activity that regulates patterning of the limb/fin along the anterio-posterior (A-P) axis[MP:0012528]
A zone of polarizing activity that is part of a pectoral appendage bud mesenchyme.
A small group of mesodermal cells located at the posterior margin of the developing fin bud. the ZPA is thought to produce retinoic acid and thereby provides positional information to the developing bud. Gibert et al., 2006.[TAO]
zone of polarizing activity pectoral fin bud
zone of polarizing activity of pectoral appendage
A zone of polarizing activity that is part of a pelvic appendage bud mesenchyme.
zone of polarizing activity pelvic fin bud
zone of polarizing activity of pelvic appendage
A limb bud that develops into a forelimb.
Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995)
A limb bud that develops into a hindlimb.
The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO]
Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick.
A limb bud that develops into a forelimb or pectoral fin.
Fin bud that develops into the pectoral fin.[TAO]
at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future
A limb bud that develops into a hindlimb or pelvic fin.
Fin bud that develops into the pelvic fin.[TAO]
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
An apical ectodermal ridge that is part of a pectoral appendage bud.
An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]
Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]
apical ectodermal ridge pectoral fin bud
pectoral appendage apical ectodermal ridge
An apical ectodermal ridge that is part of a pelvic appendage bud.
An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]
pelvic appendage apical ectodermal ridge
Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium.
presumptive retinal pigmented epithelium
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)
A pancreatic duct that develops from the dorsal pancreatic bud.
Most humans have just one pancreatic duct. However, some have an additional accessory pancreatic duct also called the Duct of Santorini, which connects straight to the duodenum at the minor duodenal papilla. Both these ducts connect to the second part (the vertical one) of the duodenum. However, the Duct of Santorini, which bypasses the Ampulla of Vater, is non-functional whereas the Duct of Wirsung is functional and carries the digestive enzymes released by the pancreas. It is named for Giovanni Domenico Santorini
A loop of nerves that are part of the cervical plexus that lies superficial to the internal jugular vein in the carotid sheath. Branches from the ansa cervicalis innervate three of the four infrahyoid muscles, including the sternohyoid muscle, the sternothyroid muscle, and the omohyoid muscle.
In human anatomy, the anterior spinal artery is the blood vessel that supplies the anterior portion of the spinal cord. It arises from branches of the vertebral arteries and is supplied by the anterior segmental medullary arteries, including the artery of Adamkiewicz, and courses along the anterior aspect of the spinal cord.
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
peripheral part of autonomic nervous system
Obsoleted as our current model is to treat the entire ANS as being part of the PNS
peripheral part of autonomous nervous system
The cisterna chyli (or cysterna chyli, and etymologically more correct, receptaculum chyli) is a dilated sac at the lower end of the thoracic duct into which lymph from the intestinal trunk and two lumbar lymphatic trunks flow.
In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:
The conus medullaris is the terminal end of the spinal cord. It occurs near lumbar vertebral levels 1 (L1) and 2 (L2). After the spinal cord tapers out, the spinal nerves continue as dangling nerve roots called cauda equina. This terminal nerve root tail is referred to as the filum terminale. The upper end of the conus medullaris is usually not well defined.
The conical end of the spinal cord, which continues with the filum terminale. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
the short trunk that recieves most of the cardiac veins carrying the blood from the myocardium and delivers it to the right atrium, with the sinoatrial connection occurring between the inferior vena cava and the atrioventricular orifice
The sinus, before entering the auricle, is considerably dilated - nearly to the size of the end of the little finger. Its wall is partly muscular, and at its junction with the great coronary vein is somewhat constricted and furnished with a valve consisting of two unequal segments
A fetal blood vessel connecting the pulmonary artery with the descending aorta[MESH]. In the developing fetus, the ductus arteriosus is a shunt connecting the pulmonary artery to the aortic arch. It allows most of the blood from the right ventricle to bypass the fetus' fluid-filled lungs, protecting the lungs from being overworked and allowing the left ventricle to strengthen. There are two other fetal shunts, the ductus venosus and the foramen ovale[MP]. the fetal vessel that connects the left pulmonary artery with the descending aorta; the ductus arteriosus normally regresses into a fibrous cord, the ligamentum arteriousum after birth[MP]
The temporary channel or blood vessel between the aorta and pulmonary artery in the fetus. [TFD][VHOG]
The Intercostales externi (External intercostals) are eleven in number on either side. They extend from the tubercles of the ribs behind, to the cartilages of the ribs in front, where they end in thin membranes, the anterior intercostal membranes, which are continued forward to the sternum. Each arises from the lower border of a rib, and is inserted into the upper border of the rib below. In the two lower spaces they extend to the ends of the cartilages, and in the upper two or three spaces they do not quite reach the ends of the ribs. They are thicker than the Intercostales interni, and their fibers are directed obliquely downward and laterally on the back of the thorax, and downward, forward, and medially on the front (the example is often used of sticking one's hands in their pocket and noting the direction of the fingers pointing downward and medially).
The external oblique muscle (of the abdomen) (also external abdominal oblique muscle) is the largest and the most superficial (outermost) of the three flat muscles of the lateral anterior abdomen.
A strand of fibrous tissue in the spinal cord consisting of the filum terminale internum and the filum terminale externum.
definition to be verified, wikipedia def conflicts with VHOG?
The slender, thread-like continuation of the spinal cord below the origin of the lumbar nerves. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
A segment of autopod that is part of a pes.
The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.
A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [http://en.wikipedia.org/wiki/Foramen_rotundum][VHOG]
It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG]
The greater omentum (also the great omentum, omentum majus, gastrocolic omentum, epiploön, or, especially in animals, caul) is a large fold of peritoneum that hangs down from the stomach, and extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
A filmy, transparent double fold of the peritoneum, draping the transverse colon and coils of the small intestine. It is attached along the greater curvature of the stomach and the first part of the duodenum. [TFD][VHOG]
peritoneum of the peritoneal cavity proper
The cavity in the abdomen that is inside the peritoneum but outside of the lesser sac. [WP,unvetted].
A segment of autopod that is part of a manus.
A three-dimensional arrangement formed by plates of hepatocytes, usually one cell thick, that radiates from the center of the liver lobule; hepatic laminae are highly branched, irregular structures bordered by endothelial lined vascular spaces called hepatic sinusoids.
A ganglion located near where the inferior mesenteric artery branches from the abdominal aorta[WP].
The internal oblique muscle (of the abdomen) is the intermediate muscle of the abdomen, lying just underneath the external oblique and just above (superficial to) the transverse abdominal muscle.
Either of the anterior and posterior grooves on the surface of the heart that lie over the interventricular septum and join at the apex.
The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side
Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO]
One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary]
relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO]
A thymus lobe that is in the left side of a thymus.
An umbilical vein that is in the left side of a multicellular organism.
A vitelline vein that is in the left side of a multicellular organism.
An axial muscle that originates in the cervical vertebraae inserts on the scapula.
Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA].
overlaps with region sometimes called 'loin'
A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae.
The median sacral artery (or middle sacral artery) is a small vessel, which arises from the back of the aorta, a little above its bifurcation. It descends in the middle line in front of the fourth and fifth lumbar vertebræ, the sacrum and coccyx, and ends in the glomus coccygeum (coccygeal gland). From it, minute branches are said to pass to the posterior surface of the rectum. On the last lumbar vertebra it anastomoses with the lumbar branch of the iliolumbar artery; in front of the sacrum it anastomoses with the lateral sacral arteries, and sends offsets into the anterior sacral foramina. It is crossed by the left common iliac vein, and is accompanied by a pair of venæ comitantes; these unite to form a single vessel, which opens into the left common iliac vein.
The obturator nerve arises from the ventral divisions of the second, third, and fourth lumbar nerves; the branch from the third is the largest, while that from the second is often very small.
The platysma is a pharyngeal arch 2 muscle and a superficial facial muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical branch of the facial nerve. It attaches to the mandible and it attaches to the skin of the head, neck, and thoracic region where it is found superficial to the clavicle. Burrows et al. (2011) argue that in hylobatids (and, presumably, other primates) the platysma in the region of the modiolus represents both the cervicale and myoides muscles.
The platysma is a pharyngeal arch 2 muscle and a superficial facial muscle that participates in oral/pharyngeal behaviors and is innervated by the cervical branch of the facial nerve, and attaches to the skin.[FEED]
One of these (facial muscles in mammals), the platysma, is an unspecialized muscle derived from the hyoid arch.[well established][VHOG]
Human variation notes: Variations occur in the extension over the face and over the clavicle and shoulder; it may be absent or interdigitate with the muscle of the opposite side in front of the neck; attachment to clavicle, mastoid process or occipital bone occurs. A more or less independent fasciculus, the occipitalis minor, may extend from the fascia over the trapezius to fascia over the insertion of the sternocleidomastoideus.
A thymus lobe that is in the right side of a thymus.
An umbilical vein that is in the right side of a multicellular organism.
A vitelline vein that is in the right side of a multicellular organism.
A subdivision of an organism along the anterior-posterior axis in the pelvic region immediately posterior to the lumbar region and anterior to the caudal region. Sometimes an intermediate region is defined between the sacral and caudal.
Amphibians - 1 sacral vertebra; Living reptiles & most birds - 2 sacral vertebrae; Most mammals - 3 to 5 sacral vertebrae. TODO - split sacral from sacrococcygeal
A portion of the lateral venous sinus, bulging prominently into the mastoid cavity, that serves as a principal conduit by which blood leaves the cranium[EPIC]. The sigmoid is drained by the internal jugular vein
The sigmoid sinuses, within a human head, are 2 areas beneath the brain, which allow blood veins to span the area, from the center of the head downward. They drain from the transverse sinuses (under the back of the brain) to the internal jugular vein. Each sigmoid sinus begins beneath the temporal bone and follows a tortuous course to the jugular foramen, at which point the sinus becomes continuous with the internal jugular vein[Wikipedia:Sigmoid_sinus].
trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami.
A simple columnar epithelium that is part of a fundus of stomach.
A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD].
neural tube lateral wall sulcus limitans
In the upper part of the superior mesenteric plexus close to the origin of the superior mesenteric artery is a ganglion, the superior mesenteric ganglion. The superior mesenteric ganglion is the synapsing point for one of the pre- and post-synaptic nerves of the sympathetic division of the autonomous nervous system. This nerve goes on to innervate part of the large intestine.
The orbital fissure that is situated superiorly between the greater wing and the lesser wing of the sphenoid bone
An unpaired venous dural sinus that receives blood from the superior cerebellar veins and inferior sagittal sinus and drains into the confluence of sinuses.
A cardiac valve leaflet that is part of a tricuspid valve.
The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG]
the semicircular fold of endocardium located on the right atrium at the point of attachment of the inferior vena cava; during development this valve helps direct the flow of oxygen-rich blood through the right atrium into the left cardiac atrium via the foramen ovale (preventing blood flowing into the right ventricle)
this class should be subdivided into the embryonic structure and the vestigial adult remnant, a small endocardialfold
A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein.
the paired veins that carry blood from the yolk sac back to the embryo
One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO]
Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG]
check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO
The superior mesenteric plexus is a continuation of the lower part of the celiac plexus, receiving a branch from the junction of the right vagus nerve with the plexus. It surrounds the superior mesenteric artery, accompanies it into the mesentery, and divides into a number of secondary plexuses, which are distributed to all the parts supplied by the artery, viz. , pancreatic branches to the pancreas; intestinal branches to the small intestine; and ileocolic, right colic, and middle colic branches, which supply the corresponding parts of the great intestine. The nerves composing this plexus are white in color and firm in texture; in the upper part of the plexus close to the origin of the superior mesenteric artery is the superior mesenteric ganglion.
The ventricles of the heart are separated by two grooves, one of which, the anterior longitudinal sulcus (or anterior interventricular sulcus), is situated on the sternocostal surface of the heart, close to its left margin. The other groove separating the ventricles is the posterior interventricular sulcus.
The ventricles are separated by two grooves, one of which, the anterior longitudinal sulcus, is situated on the sternocostal surface of the heart, close to its left margin, the other posterior longitudinal sulcus (posterior interventricular sulcus, inferior interventricular groove), on the diaphragmatic surface near the right margin. In it run the posterior interventricular artery and middle cardiac vein.
Cranial neural crest which gives rise to the glossopharyngeal ganglion.
A blood vessel that is associated with the lens. In mammals, this is transient and normally nourishes the retina, immature lens and primary vitreous of the developing eye.
we are currently conflating vessel and vasculature - we may wish to split this class - see also vascular plexus term. The ZFA class represents the vasculature
One of a group of muscles used in mastication and swallowing. These muscles are attached to the hyoid bone, which is suspended in the neck and forms the base of the tongue and larynx. The muscles are divided into suprahyoid (superior) or infrahyoid (inferior) groups relative to the bone[WP, generalized].
Although the zebrafish occupies a rather derived phylogenetic position within actinopterygians and even within teleosts, with respect to the mandibular, hyoid and hypobranchial muscles it seems justified to consider it an appropriate representative of these two groups. Among these muscles, the three with clear homologues in tetrapods and the further three identified in sarcopterygian fish are particularly appropriate for comparisons of results between the actinopterygian zebrafish and the sarcopterygians.[well established][VHOG]
attachment sites may vary by species; for example, in orangutans, the posterior digastric does not attach to the hyoid, but we may still consider this a (supra)hyoid muscle.
Portion of tissue on the side of the lumen of the neural tube.
In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). Editor note: todo - epidermis? todo - track down EHDAA2 class in new release
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
Hindbrain segment or neuromere. Kimmel et al, 1995.[TAO]
A neural tube lateral wall that is part of a rhombomere.
the third transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
the fourth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
the fifth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
the sixth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
the seventh transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
the eighth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
Lateral wall that is part of the telencephalon. [Bgee_curator][VHOG]
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID].
we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution.
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]
variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals
Cranial neural crest which gives rise to the trigeminal ganglion.
todo - compare ZFA and EHDAA2 representation
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Cranial neural crest that gives rise to the facio-acoustic ganglion.
A rhombomere lateral wall that is part of a rhombomere 1.
A rhombomere roof plate that is part of a rhombomere 1.
the second transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order
A rhombomere floor plate that is part of a rhombomere 2.
A rhombomere lateral wall that is part of a rhombomere 2.
A rhombomere roof plate that is part of a rhombomere 2.
A rhombomere floor plate that is part of a rhombomere 3.
A rhombomere lateral wall that is part of a rhombomere 3.
A rhombomere roof plate that is part of a rhombomere 3.
A rhombomere floor plate that is part of a rhombomere 4.
A rhombomere lateral wall that is part of a rhombomere 4.
A rhombomere roof plate that is part of a rhombomere 4.
A rhombomere floor plate that is part of a rhombomere 5.
A rhombomere lateral wall that is part of a rhombomere 5.
A rhombomere roof plate that is part of a rhombomere 5.
A rhombomere floor plate that is part of a rhombomere 6.
A rhombomere lateral wall that is part of a rhombomere 6.
A rhombomere roof plate that is part of a rhombomere 6.
A rhombomere floor plate that is part of a rhombomere 7.
A rhombomere lateral wall that is part of a rhombomere 7.
A rhombomere roof plate that is part of a rhombomere 7.
A rhombomere floor plate that is part of a rhombomere 8.
A rhombomere lateral wall that is part of a rhombomere 8.
A rhombomere roof plate that is part of a rhombomere 8.
Somite located in the head region, caudal to the otic vesicle
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
A region formed by non-ampulated ends of posterior and superior semicircular canals of vestibular apparatus in inner ear.
The part of the mesocardium dorsal to the embryonic heart; it breaks down to form the transverse sinus of the pericardium.
The mesentery of the embryonic heart. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum.
The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]
A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]
The second arch becomes the hyoid artery, which is prominent in early development and normally persists as the caroticotympanic branch of the ICA[Padget]
Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery
this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods
we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific
Any of the three veins including the common, external and internal iliac veins.
A corner of the medial (inner) part of an eye.
The angle at the end of the palpebral fissure, the slit between the eyelids, close to the nose. [ISBN10:0124020607, p.263][VHOG]
One of a group of arteries that supply the area between the ribs ('costae'), called the intercostal space.
TODO - add children. Mouse has dorsal, ventral and upper; humans have anterior, posterior; teleost has segmental
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
Contributes to the arch of aorta in humans
One of the 4 layers of the crystalline lens. It is found between the anterior surface of the capsule and the cortex. It is simple cuboidal epithelium responsible for creating new cells for the lens.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
Arteries which arise from the abdominal aorta and distribute to most of the intestines.
includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries
A vein that returns blood from the intestines.
In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein
The outgrowths of the embryonic maxillary prominences that come together during prenatal development to form the secondary palate
consider splitting into embryonic/fully formed
The outgrowths of the embryonic maxillae that come together during prenatal development to form the secondary palate. [TFD][VHOG]
The part of the palate formed from the intermaxillary segment.
The shelf separating the oral and nasal cavities that is formed during early embryonic development from protrusions of tissue between the olfactory pits. [TFD][VHOG]
Early tetrapod possessed a primary palate that included the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. Therapsid evolved a partial secondary palate formed by the medial extension of the premaxilla and maxilla. Mammals have a secondary palate that, in addition to extensions of the premaxilla and maxilla, includes part of the palatine bone[VHOG]
A rhombus-shaped muscle associated with the scapula and chiefly responsible for its retraction. There are two rhomboid muscles.
the valves that gate the flow of blood from the ventricles into the aorta and pulmonary trunk
Artery that supplies blood to the adrenal glands.
The cavity formed by the tubotympanic recess epithelium.
Ventral mesentery is the part of the peritoneum closest to the navel.
The mesentery that originates from the ventral side of the peritoneal cavity.[TAO]
The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG]
"The primitive gut is enveloped by a mesentery that has a dorsal and a ventral aspect. The ventral mesentery degenerates during development with the exception of the foregut ventral mesentery, which develops into specialized structures (see foregut embryology)" [http://sprojects.mmi.mcgill.ca/embryology/gi/pgm.htm]. todo - check
The ileal arteries feed oxygenated blood into the ileum, a portion of the small intestine in mammals, reptiles, and birds. They are branches of the superior mesenteric artery.
ileal branch of superior mesenteric artery
A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part.
In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system].
The amnion and chorion which surround and protect a developing fetus.
TODO - merge with extraembryonic membrane?
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN10:0073040584 (Vertebrates, Kardong)]
An epithelium that is part of a pylorus.
An epithelium that is part of a anterior chamber of eyeball.
An epithelium that is part of a upper lobe of right lung.
An epithelium that is part of a lower lobe of right lung.
An epithelium that is part of a ear vesicle.
An epithelium that is part of a ultimobranchial body.
in EHDAA2, develops_from ventral 4th arch branchial pouch endoderm. Kardong: develops from 5th pouch. http://www.ncbi.nlm.nih.gov/pubmed/16313389: the most posterior pouch generates the ultimobranchial bodies in most vertebrate classes, mammals do not form this structure.
An epithelium that is part of a duodenum of foregut.
An epithelium that is part of a duodenum of midgut.
An epithelium that is part of a manual digit 2.
An epithelium that is part of a manual digit 3.
An epithelium that is part of a manual digit 4.
An epithelium that is part of a manual digit 5.
An epithelium that is part of a pedal digit 2.
An epithelium that is part of a pedal digit 3.
An epithelium that is part of a pedal digit 4.
An epithelium that is part of a pedal digit 5.
A dental epithelium that is part of a upper jaw molar.
A dental epithelium that is part of a lower jaw molar.
An epithelium that is part of a right lung accessory lobe.
An epithelium that is part of a lens vesicle.
An epithelium that is part of a crus commune.
An epithelium that is part of a secondary palatal shelf.
An epithelium that is part of a primary palate.
An ectoderm that is part of a pharyngeal arch 2.
In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]
An ectoderm that is part of a pharyngeal arch 3.
An ectoderm that is part of a pharyngeal arch 4.
An endoderm that is part of a pharyngeal arch 2.
An endoderm that is part of a pharyngeal arch 3.
An endoderm that is part of a pharyngeal arch 4.
A mesothelium that is part of a peritoneal cavity.
A mesothelium that is part of a greater omentum.
A mesothelium that is part of a greater sac.
An endothelium that is part of a right lung.
An endothelium that is part of a left lung.
An endothelium that is part of a upper lobe of right lung.
An endothelium that is part of a lower lobe of right lung.
An endothelium that is part of a right lung accessory lobe.
A segmental bronchus that is part of a upper lobe of right lung.
right lung cranial lobe segmental bronchus
A segmental bronchus that is part of a lower lobe of right lung.
right lung caudal lobe segmental bronchus
A segmental bronchus that is part of a right lung accessory lobe.
right lung accessory lobe segmental bronchus
A bronchiole that is part of a upper lobe of right lung.
A bronchiole that is part of a right lung accessory lobe.
obsolete telencephalon lateral ventricle
A dorsal mesentery that is part of a midgut.
A dorsal mesentery that is part of a caecum.
A orbitosphenoid endochondral element that is composed primarily of a cartilage tissue.
An anatomical cavity that is part of a lens vesicle.
Mesenchyme that is part of a pharyngeal arch 2.
Mesenchyme that is part of a pharyngeal arch 3.
Mesenchyme that is part of a pharyngeal arch 4.
Mesenchyme that is part of a developing manual digit 2.
Mesenchyme that is part of a developing manual digit 3.
Mesenchyme that is part of a developing manual digit 4.
Mesenchyme that is part of a developing manual digit 5.
Mesenchyme that is part of a developing pedal digit 2.
Mesenchyme that is part of a developing pedal digit 3.
Mesenchyme that is part of a developing pedal digit 4.
Mesenchyme that is part of a developing pedal digit 5.
An odontogenic papilla that is part of a upper jaw molar.
An odontogenic papilla that is part of a lower jaw molar.
Mesenchyme that is part of a optic eminence.
Mesenchyme that is part of a developing secondary palatal shelf.
Mesenchyme that is part of a developing primary palate.
obsolete central nervous system cranial ganglion
An odontogenic papilla that is part of a upper jaw incisor.
An odontogenic papilla that is part of a lower jaw incisor.
A dental epithelium that is part of a upper jaw incisor.
A dental epithelium that is part of a lower jaw incisor.
A mesentery of duodenum that is part of a foregut.
A mesentery of duodenum that is part of a midgut.
An apical ectodermal ridge that is part of a footplate.
A venous system that is part of a hindbrain.
A mesoderm that has_potential_to_develop_into a pronephros.
Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", http://www.ncbi.nlm.nih.gov/pubmed/10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
The nephrotome is a section of the mesoderm. It gives rise to the pronephros and eventually to the rest of the kidney. A nephrotome is an obsolete term used to describe rounded mesodermal portions of the forming pronephros. In old texts the pronephros is described as forming through the fusion of multiple nephrotomes. Modern visualization methods such as scanning electron microscopy, in situ hybridization and confocal microscopy, combined with the simple approach of peeling off the epidermis to see the forming kidney, have shown that this is not the case. Nephric mesenchyme separates from the intermediate mesoderm as a single elongated primordia. As this primordia begins to undergo epithelialization the anterior portions of the pronephros form rounded protrusions, which then later become the dorsal branches of the pronephros that link to nephrostomes (distinct from nephrotomes). These rounded bumps are probably the structures observed in histological sections that are referred to as nephrotomes. Nephrostomes are thin ciliated funnels that link pronephric nephrons to the ceolom, and are not related to nephrotomes.
A multi-tissue structure that is part of a spinal cord and is part of a floor plate.
A tissue that is part of a spinal cord and is part of a roof plate.
Roof plate that is part of the spinal cord. [Bgee_curator][VHOG]
A sensory system that is capable of olfacttion (the sensory perception of smell).
consider splitting into main and accessory. See also: vomeronasal organ
we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system
The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system].
The sensory system used for olfaction (the sense of smell).[AAO]
In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].
Obsoleted definition: In the developing vertebrate embryo, the somitomeres are loose masses of paraxial mesoderm derived cells that form along each side of the neural tube towards the end of the third gestational week. The approximately 50 pairs of somitomeres begin developing in the cranial (head) region, continuing in a caudal (tail) direction until the end of week four[WP].
Around the same time that experimental embryology in avian systems was most productive in the context of vertebrate head development, researchers examining embryonic head morphology with the scanning electron microscope introduced the idea of cephalic 'somitomeres'. By removing the surface ectoderm from the head, they reported that the paraxial mesoderm was organized into pseudosegmental units resembling incompletely differentiated somites, which they called somitomeres (Meier 1979; Jacobson 1988, 1993; Jacobson and Meier 1984). Since then, however, there has been no clear evidence for somitomeres. It remains unclear how they relate to the epithelial cysts in the head mesoderm - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895339/]
A limb/fin field that has_potential_to_develop_into a pectoral appendage bud mesenchyme.
Embryonic region that develops into the pectoral fin bud.[TAO]
pectoral appendage field of lateral plate mesoderm
A limb/fin field that has_potential_to_develop_into a pelvic appendage bud mesenchyme.
Embryonic region that develops into the pelvic fin bud.[TAO]
pelvic appendage field of lateral plate mesoderm
A limb/fin field that has_potential_to_developmentally_contribute_to a paired fin bud.
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
limb/fin field of lateral plate mesoderm
A ring of cells capable of forming a limb.
the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29].
Multi-tissue structure that is the external layer of the swim bladder that is covered by the peritoneum, and made of elastic fibres and ichthyocol (short needles of collagen).
the primary reason this term is manifest in uberon to disambiguate from a structure with the same/similar name
Multi-tissue structure that is the internal layer of the swim bladder and is comprised of thin endoderm and a smooth muscle layer called the muscularis mucosa with longitudinal and circular fibres with some collagen.
A tunica intima that is part of a artery.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
this class was originally added to account for some definitions of the CNS that includes retina. Most existing AOs use CNS to exclude the retina (ZFA retina NOT part_of CNS. XAO excludes retina in text def, retina (previously) part_of CNS. MA retina NOT part_of CNS. NIF_GA retina NOT part_of CNS. Fly also excludes it. EFO also excludes it. GO also excludes it). Whilst logically valid, the use case is better served by following the developmental relationships for retina. See: http://groups.google.com/group/pons-representation-and-deployment/browse_thread/thread/957da161a4dd4f85/a340e30cc8e9b2ce?lnk=gst&q=retina#a340e30cc8e9b2ce
obsolete central nervous system plus retina
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery[MP]. The optic foramen is the opening to the optic canal. The superior surface of the sphenoid bone is bounded behind by a ridge, which forms the anterior border of a narrow, transverse groove, the chiasmatic groove (optic groove), above and behind which lies the optic chiasma; the groove ends on either side in the optic foramen, which transmits the optic nerve and ophthalmic artery (with accompanying sympathetic nerve fibres) into the orbital cavity. The left and right optic canals are 25mm apart posteriorly and 30mm apart anteriorly. They are funnel-shaped (narrowest anteriorly).
An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG]
Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO]
embryonic fibrovascular mesodermal tissue located between the optic cup and lens vesicle that normally regresses during the development of the vitreous body[MP]
Acellular in EHDAA2, MP defs says tissue
The capillary loops of the kidney that normally function as a filtration unit[MP].
...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus
A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP]
TODO - check this. BTO has podocytes under here
Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO]
The inner, or visceral, layer of the renal glomerular capsule, overlying the capillaries, composed of podocytes, and separated from the outer, or parietal, layer by the capsular (Bowman's) space[BTO]. Lies just above the thickened glomerular basement membrane and is made of podocytes. Beneath the visceral layer lie the glomerular capillaries[WP]. inner layer of the glomerular capsule surrounding the capillary endothelial cells and composed of highly specialized epithelial cells (podocytes) that are separated by filtration slits; the visceral layer is separated from the outer parietal layer by the urinary space (also known as the Bowman's or capsular space)[MP]
TODO - check - the BTO class 'glomerular epithelium' is the visceral layer. But GO uses 'glomerular epithelium' as the mereological sum of P+V layers
inner epithelial layer of Bowman's capsule
The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.
The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.
The ridge of mesoderm covered with endoderm that in the early developing embryo partitions the endodermal cloaca into the primary urogenital sinus (ventrally) and the anorectal canal of the hindgut (dorsally); the urorectal septum eventually fuses with the cloacal membrane, dividing it into a dorsal anal membrane and a larger ventral urogenital membrane - this area of fusion is represented in the adult by the perineal body[MP].
todo - use to define cloacal septation in GO
A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [TFD][VHOG]
A acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
the layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter
Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]
Middle layer of the glomerular basement membrane.
lamina densa of glomerular basement membrane
middle layer of glomerular basement membrane
Layer of the glomerular basement membrane adjacent to the glomerular capillary.
internal layer of glomerular basement membrane
lamina interna of glomerular basement membrane
Layer of the glomerular basement membrane adjacent to the podocytes and capsular space.
external layer of glomerular basement membrane
lamina externa of glomerular basement membrane
Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.
TODO - check ridge vs cord vs nephrogenic cord vs blastema
The duplex uterus is doubled, and is found in monotremes, marsupials, elephants and rodents
The bipartite uterus is y-shaped externally and divided internally (ungulates, carnivores)
The bicornate uterus is y-shaped but has no internal partition (some ungulates, whales)
The simplex uterus has only one uterine chamber (primates)
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch[BTO]. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once[GO]. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].
Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]
In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP].
Control of blood pressure is crucially dependent on the integrity of a small region of the brainstem called the ventrolateral medulla. Within this part of the brain are the cells that control the heart, blood vessels, swallowing, breathing and many other functions of the body that are not noticed at a conscious level; such unconscious activities are known as 'Autonomic'. One of these regions is the Rostral Ventrolateral Medulla (RVLM) is also known as the pressor area of the medulla (medulla pressor). It receives inhibitory GABAergic input from the caudal ventrolateral medulla (CVLM). The RVLM is the primary regulator of the sympathetic nervous system, sending excitatory fibers (catecholaminergic) to the sympathetic preganglionic neurons in the spinal cord, via reticulospinal tract[WP].
A bone tissue that is part of a long bone.
The outer or sperficial part of a bone of the manus.
The conical ventral projection on the arch of the atlas
TODO - check: anterior vs ventral; arch vs transverse process
A round nodule, small eminence, or warty outgrowth found on bones, skin, or within the lungs in tuberculosis. They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP].
A vertebral arch that is part of the first cervical vertebra
anterior costal tubercle of transverse process of cervical vertebra
tuberculum cervicales anterius vertebrae
anterior tubercle of transverse process of cervical vertebra
posterior costal tubercle of transverse process of cervical vertebra
tuberculum cervicales posterius vertebrae
posterior tubercle of transverse process of cervical vertebra
An anatomical structure that is regional part of the central nervous system where there is a significant bend of the axis.
A sharp, ventrally concave bend in the developing midbrain of the embryo[MP].
Ventral bend in the brain occurring caudal to the adenohypophyseal placode.[TAO]
A ventrally concave flexure of the embryonic brain occurring at the junction of hindbrain and spinal cord[MP].
In humans develops by the 5th week of gestation
A dorsally concave bend of the embryonic rhombencephalon that produces a thinning of the roof of the pons and medulla oblongata and defines the boundary between the metencephalon and myelencephalon in the embryo[MP].
A group of axons that are from neurons involved in proprioception from the lower trunk and lower limb[GO]. The fasciculus gracilis (tract of Goll) is a bundle of axon fibres in the dorsomedial spinal cord that carries information about fine touch, vibrations, and conscious proprioception from the lower part of the body to the brain stem. It is part of the posterior column of the spinal cord, which also contains the fasciculus cuneatus, which carries the same information from the upper part of the body. This tract and its continuation in the brain stem is often referred to as the posterior column-medial lemniscus pathway. The fasciculus gracilis is wedge-shaped on transverse section and lies next the posterior median septum, its base being at the surface of the medulla spinalis, and its apex directed toward the posterior gray commissure. It increases in size from below upward, and consists of long thin fibers that are derived from the posterior nerve roots, and ascend as far as the medulla oblongata, where they end in the nucleus gracilis. The tract of Goll was named after Swiss neuroanatomist Friedrich Goll[WP].
distinction between axon tract and fasicle is unclear
A gracile fasciculus that is part of a spinal cord.
spinal cord segment of fasciculus gracilis
spinal cord segment of gracile fasciculus
An axon tract in the spinal cord and medulla which primarily transmits information from the forelimb and trunk. It is part of the dorsal column-medial lemniscus pathway.
we assign the synonym 'Burdachs tract' to the subclass. sometimes the term 'cuneate fasciculus' refers specifically to cuneate fasiculus of spinal cord. We use the term more broadly here.
An axon tract in the spinal cord which primarily transmits information from the forelimb and trunk. It is part of the posterior column-medial lemniscus pathway.
check ontology structure, isa parentage to fasciculus of spinal cord should be inferred. TODO - change definition to be the *whole* of the CF in the SC
A fascicle that is part of a spinal cord.
A subdivision of spinal cord dorsal column that is part of a thoracic spinal cord.
dorsal funiculus of thoracic segment of spinal cord
dorsal white column of thoracic segment of spinal cord
thoracic segment of dorsal funiculus of spinal cord
A subdivision of spinal cord dorsal column that is part of a sacral spinal cord.
sacral subsegment of dorsal funiculus of spinal cord
A subdivision of spinal cord dorsal column that is part of a cervical spinal cord.
cervical segment of dorsal funiculus of spinal cord
dorsal funiculus of cervical segment of spinal cord
dorsal white column of cervical segment of spinal cord
A subdivision of spinal cord dorsal column that is part of a lumbar spinal cord.
dorsal funiculus of lumbar segment of spinal cord
dorsal white column of lumbar segment of spinal cord
lumbar segment of dorsal funiculus of spinal cord
lumbar segment of gracile fasciculus of spinal cord
A spinal cord segment that adjacent_to a sacral region.
segmenta sacralia medullae spinalis [1-5]
This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term
A spinal cord segment that adjacent_to a caudal region.
segmenta coccygea medullae spinalis [1-3]
for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned
A subdivision of spinal cord lateral column that is part of a thoracic spinal cord.
A subdivision of spinal cord lateral column that is part of a sacral spinal cord.
A subdivision of spinal cord lateral column that is part of a cervical spinal cord.
A subdivision of spinal cord lateral column that is part of a lumbar spinal cord.
A subdivision of spinal cord ventral column that is part of a thoracic spinal cord.
A subdivision of spinal cord ventral column that is part of a sacral spinal cord.
A subdivision of spinal cord ventral column that is part of a cervical spinal cord.
A subdivision of spinal cord ventral column that is part of a lumbar spinal cord.
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
the paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw
From the lower border of the inferior nasal concha, a thin lamina, the maxillary process, curves downward and lateralward; it articulates with the maxilla and forms a part of the medial wall of the maxillary sinus.
maxillary process of inferior nasal turbinate
processus maxillaris (concha nasalis inferior)
processus maxillaris conchae nasalis inferioris
p. maxillaris conchae nasalis inferioris
maxillary process of inferior nasal concha
An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO].
we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode
By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit].
A thick, horizontal process of the maxilla. It forms the anterior three quarters of the hard palate, the horizontal plate of the palatine bone making up the rest.
A groove that is situated between the 1st and 2nd pharyngeal arch.
In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]
A groove that is situated between the 2nd and 3rd pharyngeal arch.
A groove that is situated between the 3rd and 4th pharyngeal arch.
A groove that is situated between the 4th and 5th pharyngeal arch.
the embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin
The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG]
embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]
In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG]
GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771]
we assume the EMAPA class is the undifferentiated form based on TS timings
An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches.
Note we use overlaps as the relationship to the arches
A rudimentary additional digit-like structure on the preaxial side of the thumb of certain amphibians and mammals[dictionary.com].
Two or more elements located ventral and medial to the metacarpal of digit II(I). The proximal prepollex is small and round whereas distal prepollex 1 is usually large and wedge-shaped. When more elements are present, they are smaller than previous elements.[AAO]
not homologous to digit 1 of tetrapods. Note we treat the prepollex as distinct from the digits, which are not part of the carpus
encompasses digits and prepollex. requires review
The mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses.
TODO - expand subtypes post EHDAA2-revision, check lateral wall
A subdivision of skeleton that subdivision_of a pharyngeal arch 2.
it's not clear where AAO:'hyobranchial skeleton' belongs
A subdivision of skeleton that subdivision_of a post-hyoid pharyngeal arch.
Skeletal and cartilage elements of the gill arches; the last five of the set of seven pharyngeal arches; the numbering system can be confusing; generally branchial arch #1 is the first gill arch, or the third pharyngeal arch, but some authors do not follow this convention. Kimmel et al, 1995.[TAO]
XAO class belongs here, as it clearly refers to arches 3-7. In ZFA this is part_of the pharyngeal arches, but we retain this structure to refer to the embryonic structure
The epithelial lining of the surface of the coelom.
EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium'
The mesonephric equivalent of the ascending limb, or straight distal segment, of metanephric nephrons.
A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx
OBSOLETE: A leg is a limb on which an animal walks and stands (GO:0035110).
this class was originally introduced to support GO:0035110, but this has been obsoleted, because leg is a mechano-functional grouping
The walking appendages of each segment of the ventral adult external thorax[FBbt]. A leg derived from an imaginal disc[GO].
A jointed or prehensible appendage used for locomotion or manipulation. Examples: human arm, human leg, octopus tentacle, insect limb[Wikipedia]. A limb is an appendage of an animal used for locomotion or grasping. For example a leg, arm or some types of fin[GO].
this class was originally introduced to account for the previously vague use of the term 'limb' in GO.
A bone that is part of the manus skeleton. Note that this includes the carpal bones.
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP].
ductus excretorius glandulae vesiculosae
Any of the ducts that are part of a male reproductive system.
this class groups the individual ducts in a variety of species
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
Serous sac, which has as parts the conjunctiva and the cavity of conjunctiva. Examples: There are only two conjunctival sacs, the right and the left.[FMA]
Multilaminar epithelium, which of consists of more than one layer of epithelial cells, in contact with a basement membrane, that can undergo distention and contraction without losing its integrity and consistency. Examples: urothelium.[FMA]
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
An urothelium of ureter that is part of a mucosa of major calyx.
A thin bony plate occasionally found projecting from the inner wall of the ethmoid labyrinth, above the bony superior nasal concha, and the mucous membrane covering the plate.
The back part of the medial surface of the labyrinth of ethmoid is subdivided by a narrow oblique fissure, the superior meatus of the nose, bounded above by a thin, curved plate, the superior nasal concha. The bone found in superior nasal concha is part of the ethmoid bone.
The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.
The inferior nasal concha (Inferior Turbinated Bone) is one of the turbinates in the nose. It extends horizontally along the lateral wall of the nasal cavity [Fig. 1] and consists of a of spongy bone, curled upon itself like a scroll. Each inferior nasal concha is considered a facial pair of bones since they arise from the maxillae bones and projects horizontally into the nasal cavity. They are also termed 'inferior nasal turbinates' because they function similar to that of a turbine. As the air passes through the turbinates, the air is churned against these mucosa-lined bones in order to receive warmth, moisture and cleansing. Superior to inferior nasal concha are the middle nasal concha and superior nasal concha which arise from the cranial portion of the skull. Hence, these two are considered as a part of the cranial bones. It has two surfaces, two borders, and two extremities.
in FMA this is not classified with the other turbinates. In Uberon we subdivide the turbinates into the ethmoturbinates and the inferior turbinate. EDITOR NOTE: TODO check ethmoidal process of inferior nasal concha
Behind the lacrimal process of the inferior nasal conchae lies a broad, thin plate, the ethmoidal process, which ascends to join the uncinate process of the ethmoid; from its lower border a thin lamina, the maxillary process, curves downward and lateralward; it articulates with the maxilla and forms a part of the medial wall of the maxillary sinus.
ethmoidal process of inferior nasal turbinate
processus ethmoidalis (concha nasalis inferior)
processus ethmoidalis conchae nasalis inferioris
ethmoidal process of inferior nasal concha
A naris that provides one of the small external openings of the head that give passage to air for breathing.
Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO]
relationship loss: subclass nasal opening (AAO:0000316)[AAO]
In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG]
Fish have two pairs of external nostrils.
initial opening of the nasal pits and olfactory sac of the embryo into the rostral part of the primordial oronasal cavity, before the formation of the secondary palate.
TODO - check. MA says part_of external naris.
The lower segment of the hair that circles the dermal papilla and the hair matrix.
see https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376
A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP].
It surrounds the hair follicle like a sleeve all the way to the bulb. The outer root sheath is essentially a stratified epithelium that is contiguous with the epidermis.
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
An outflow tract that is part of a cardiac atrium.
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]
An outflow tract of atrium that is part of a left atrium.
One of the pair of spiral mesenchymal swellings in the primordial ventricular outflow tract, that eventually fuse to form the conotruncal septum, dividing the subvalvular outflow tract and contributing to the membranous interventricular septum[MP]
The portion of the hair follicle from the entrance of the sebaceous gland duct to the surface opening.
A fenestrated endothelial-like tissue situated at the intersection of the cornea and the iris[GO]. The trabecular meshwork is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). The tissue is spongy and lined by trabeculocytes; it allows fluid to drain into a set of tubes called Schlemm's canal flowing into the blood system[WP]. A porelike structure surrounding the entire circumference of the anterior chamber through which aqueous humor circulates to the canal of Schlemm.[GAID] the pore-like structure surrounding the entire circumference of the anterior chamber through which aqueous humor circulates[MP].
ligamentum pectinatum anguli iridocornealis
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP]
A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
A triangular, fluid-filled space normally found between the inner and outer rows of supporting pillar cells in the organ of Corti.
The function of the group of barriers and transport systems which regulate the transport of various substances from blood to inner ear tissue and maintain the microhomeostasis and functional integrity of the inner ear; the endothelial cells of the inner ear blood capillaries, linked to each other by tight junctions, represent the main component of the blood-inner ear barrier
A space between the cerebellum and the dorsal surface of the medulla[MP]. The cisterna magna (or cerebellomedullary cistern) is one of three principal openings in the subarachnoid space between the arachnoid and pia mater layers of the meninges surrounding the brain. The openings are collectively referred to as cisterns. The cisterna magna is located between the cerebellum and the dorsal surface of the medulla oblongata. Cerebrospinal fluid produced in the fourth ventricle drains into the cisterna magna via the lateral apertures and median aperture. The two other principal cisterns are the pontine cistern located between the pons and the medulla, and the interpeduncular cistern located between the cerebral peduncles. Cerebral spinal fluid can also be obtained by puncture of the cisterna magna (cistern puncture).
The area located in the bottom of the permanent portion of a resting (telogen) hair follicle where the cells of the external root sheath of the hair follicle are contiguous with the basal layer of the epidermis; this portion of the follicle is involved in the generation of a new hair at the onset of the hair growth cycle (anagen) and contains the hair follicle stem cells
crus primum lobuli ansiformis cerebelli [h vii a]
first crus of ansiform lobule of cerebellum [h vii a]
crus secundum lobuli ansiformis cerebelli [h vii a
second crus of ansiform lobule of cerebellum [h vii a]
Superficial layer of the main olfactory bulb containing axons from the olfactory nerve and glial cells
the outermost layer of the olfactory bulb; consists primarily of olfactory afferent axons and ensheathing glia
olfactory bulb main olfactory nerve layer
The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium
The prominent ridges of atrial myocardium located on the inner surface of most of the right atrium and both the right and left auricular regions[MP].
The portion of the cavity of the right atrium of the heart that receives the blood from the vena cavae and is separated from the rest of the atrium by the crista terminalis
The impulse conduction tract that originates in the sinoatrial node and transmits signal to the left atrium
The layer of loose fibrous tissue located between the endocardium and myocardium which contains the nerves and the impulse-conducting system (Purkinje fibers) of the heart
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
Subdivision of conducting system of heart which enters the septal myocardium of left ventricle and is continuous with the anterior, septal and posterior divisions of the left branch of the atrioventricular bundle[FMA]. the left branch of the atrioventricular bundle that separates at the bundle of His, descends the septal wall of the left ventricle and connects to the terminal Purkinje fiber[MP].
crus sinistrum (fasciculi atrioventricularis)
Subdivision of conducting system of heart which enters the septal myocardium of right ventricle to reach the anterior papillary muscle and then subendocardially to the apex of the heart[FMA]. the right branch of the atrioventricular bundle that separates just below the bundle of His, descends the septal wall of the right ventricle and connects to the terminal Purkinje fibers[MP].
crus dextrum (fasciculi atrioventricularis)
right right crus of atrioventricular bundle
The supporting bundles of muscular fibers lining the walls of the atrial myocardium
The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve
The three fibrous triangular components and associated flap of the aortic valve
The fibrous ring of the aortic valve that attaches the cusps of aortic valve to the wall of left ventricle, and which consists of portions of the fibrous scallops of the posterior, right anterior and left anterior cusps
The three fibrous triangular components and associated flap of the pulmonary valve
The fibrous ring of the pulmonary valve that attaches the cusps of pulmonary valve to the wall of right ventricle, and which consists of portions of the fibrous scallops of the anterior, right posterior and left posterior cusps
The tendinous strands that connect the papillary muscles on the wall of the ventricles to the leaflets of the atrioventricular valves; the chordae tendineae serve to prevent the AV valves from prolapsing back into the atria
The fibrous ring of the mitral valve that attaches the cusps of mitral valve to the heart, and which consists of portions of the fibrous scallops of the anterior and posterior cusps
The two fibrous components and associated flaps of the mitral valve
The fibrous ring of the tricuspid valve that attaches the cusps of tricuspid valve to the heart, and which consists of portions of the fibrous scallops of the anterior cusp (infundibular cusp), the posterior cusp (marginal cusp), and the septal cusp (medial cusp)
The three fibrous triangular components and associated flaps of the tricuspid valve
check whether we need to separate cusp/leaflet/valve
cuspis septalis valvae atrioventricularis dextrae
septal cusp of right atrioventricular valve
septal leaflet of right-sided tricuspid valve
The paired arteries that carry blood to the yolk sac from the dorsal aorta
Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664]
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
The bulb region adjacent to the dermal papilla that contains rapidly proliferating matrix cells that give rise to the various cell lineages of the hair shaft and inner root sheath
The middle part of the hair follicle that extends from the sebaceous duct to the bulge
The posterior border of the optic nerve foramen.
The group of interneurons within the medulla oblongata's ventral respiratory group that are important for the generation of ventilatory (inspiratory) rhythmogenesis[MP]. The Pre-Bötzinger Complex (preBötC) is a cluster of interneurons in the ventrolateral medulla of the brainstem, which is essential to the generation of respiratory rhythm in mammals[WP].
pre-botzinger respiratory control center
the MP class implies this is part of both the medulla oblongata and the PSNS, which violates the spatial disjointness constraint. We weaken this to continuous_with here.
A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices
TODO - compare with ZFA atrioventricular ring, part of the conduction system
Organ component which has as its parts the cusp proper, lunule and nodule of semilunar valvule[FMA]. The cusps of the heart valves serve to seal the heart valves when closed. There are three cusps for each valve except for the mitral valve, which has only two (hence its alternate name, 'bicuspid valve'). 'Nodules' are located at the tip of the valve, to form a tighter seal[WP].
A small transparent canal running through the vitreous body from the optical nerve disc to the lens. It is formed by an invagination of the hyaloid, a membrane which encloses the vitreous body[WP].
Vein internal to the eye. Isogai et al. 2001.[TAO]
An interdigital region that is part of a manus.
interdigital region between manual digits
An interdigital region that is part of a pes.
interdigital region between pedal digits
A membranous region of skin between the digits.
Normally in mammals, webbing is present in the embryo but resorbed later in development, but in various mammal species it occasionally persists in adulthood In humans, it can be found in those suffering from LEOPARD syndrome and from Aarskog-Scott syndrome. Webbing between the digits of the hindfoot is also present in several mammals that spend part of their time in the water
Webbing accommodates movement in the water[WP]
An interdigital region that adjacent_to a digit 1 and adjacent_to a digit 2.
interdigital region between digits I and II
interdigital region between digits 1 and 2
An interdigital region that adjacent_to a digit 2 and adjacent_to a digit 3.
interdigital region between digits II and III
interdigital region between digits 2 and 3
An interdigital region that adjacent_to a digit 3 and adjacent_to a digit 4.
interdigital region between digits III and IV
interdigital region between digits 3 and 4
An interdigital region that adjacent_to a digit 4 and adjacent_to a digit 5.
interdigital region between digits IV and V
interdigital region between digits 4 and 5
An interdigital region that adjacent_to a manual digit 1 and adjacent_to a manual digit 2.
interdigital region between manual digits I and II
interdigital region between manual digits 1 and 2
An interdigital region that adjacent_to a manual digit 2 and adjacent_to a manual digit 3.
interdigital region between manual digits II and III
interdigital region between manual digits 2 and 3
An interdigital region that adjacent_to a manual digit 3 and adjacent_to a manual digit 4.
interdigital region between manual digits III and IV
interdigital region between manual digits 3 and 4
An interdigital region that adjacent_to a manual digit 4 and adjacent_to a manual digit 5.
interdigital region between manual digits IV and V
interdigital region between manual digits 4 and 5
An interdigital region that adjacent_to a pedal digit 1 and adjacent_to a pedal digit 2.
interdigital region between pedal digits I and II
interdigital region between pedal digits 1 and 2
An interdigital region that adjacent_to a pedal digit 2 and adjacent_to a pedal digit 3.
interdigital region between pedal digits II and III
interdigital region between pedal digits 2 and 3
An interdigital region that adjacent_to a pedal digit 3 and adjacent_to a pedal digit 4.
interdigital region between pedal digits III and IV
interdigital region between pedal digits 3 and 4
An interdigital region that adjacent_to a pedal digit 4 and adjacent_to a pedal digit 5.
interdigital region between pedal digits IV and V
interdigital region between pedal digits 4 and 5
A digit that is part of a digit 1 plus metapodial segment.
A digit that is part of a digit 2 plus metapodial segment.
A digit that is part of a digit 3 plus metapodial segment.
A digit that is part of a digit 4 plus metapodial segment.
A digit that is part of a digit 5 plus metapodial segment.
The occiput is the anatomical term for the posterior (back) portion of the head.
A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
The falx cerebri, also known as the cerebral falx, so named from its sickle-like form, is a strong, arched fold of dura mater which descends vertically in the longitudinal fissure between the cerebral hemispheres. It is narrow in front, where it is attached to the crista galli of the ethmoid; and broad behind, where it is connected with the upper surface of the tentorium cerebelli. Its upper margin is convex, and attached to the inner surface of the skull in the middle line, as far back as the internal occipital protuberance; it contains the superior sagittal sinus. Its lower margin is free and concave, and contains the inferior sagittal sinus. The falx cerebri is known to calcify with age.
The distal portion of Bulbus cordis that forms an outflow channel and gives rise to the proximal conus cordis.
The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta (256). However, similar to the mammalian condition (306, 326, 339), the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development (134, 135). The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis.[well established][VHOG]
A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses).
Paired processes at the cephalic and caudal ends of the neural arch. They function as interlocking structures between adjacent vertebrae, and limit dorsoventral flexion and lateral movement of the column in the trunk region[AAO]. The articular processes or zygapophyses of a vertebra, in human anatomy contain two superior and two inferior, spring from the junctions of the pedicles and laminae. These stick out of an end of a vertebra to lock with a zygapophysis on the next vertebra, to make the backbone more stable. The superior processes project upward from a lower vertebra, and their articular surfaces are directed more or less backward. The inferior processes project downward from a higher vertebra, and their articular surfaces are directed more or less forward and outward. The articular surfaces are coated with hyaline cartilage.
TODO - class as endochondral bone, check species
Paired processes at the cephalic and caudal ends of the neural arch. They function as interlocking structures between adjacent vertebrae, and limit dorsoventral flexion and lateral movement of the column in the trunk region.[AAO]
One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch.
A vertebral arch that is attached to the ventral surface or the vertebral centrum and encloses and protects the caudal artery and vein ventrally.
Bony canal attached to the ventral surface or the vertebral centrum that encloses and protects the caudal artery and vein ventrally. The arch consists of right and left halves, which are fused ventrally to give a V- or Y-shape to the ventral aspect of the vertebra.[AAO]
Hemal arches extend ventrally from the centra of caudal and transitional vertebrae to enclose the caudal artery and vein. In cyprinids, the hemal arch forms directly in membrane bone.[TAO]
In cyprinids, the hemal arch forms directly in membrane bone[ZFA]
fish, most reptiles, some birds, and some mammals with long tails.
Any collection of muscles that is part of a hindlimb zeugopod.
A bone that is part of a post-anal tail.
MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future.
Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this.
This region is reduced in humans and corresponds to the coccyx
We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud
That portion of the spine comprising the cervical vertebrae. The neck area of the spine.
Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO]
That part of the spine comprising the thoracic vertebrae.
Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]
Subdivision of vertebral column that corresponds to the lumbar subdivision of the body, containing the lumbar vertebrae.
Subdivision of vertebral column that corresponds to the sacral subdivision of the body, containing the sacral vertebrae or sacrum.
Region of the vertebral column represented by one or two vertebrae.[AAO]
In adult humans, the sacral skeleton is fused and called the sacrum
Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae.
Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO]
in AAO, this is posterior to the caudal-sacral region
A collection of all skeletal elements in some subdivision of the vertebral column.
subdivision of spinal cord lateral column
segment of dorsal funiculus of spinal cord
subdivision of spinal cord dorsal column
The fundus of gallbladder is the portion of the gallbladder which lies the farthest from the cystic duct. It is covered with peritoneum. A traditional cholecystectomy is most commonly performed from the infundibulum to the fundus. It's at the same level as the transpyloric plane.
The base or posterior surface of the urinary bladder contains the trigone of the bladder and the outlet where urine empties through the internal urethral orifice.
Region of cortex near to the rhinal sulcus. It is defined differently in different nomenclatures, due in part to the lack of agreement on the definition of the border of this region. In the rat, the perirhinal cortex occupies only caudal levels of the rhinal sulcus while in the monkey, it occurpies the full rostrocaudal extent of the rhinal sulcus (Burwell et al., Hippocampus, 5: 390-408, 1995).
The major afferent track to the habenula from the telencephalon (particularly in the septal side) in all vertebrates[Butler and Hodos].
Stria medullaris of thalamus is a slender fiber bundle on the dorsal surface of the diencephalon which terminates posteriorly in the habenular nuclei[FMA:62080].
Component of the parietal lobe. The inferior parietal cortex label includes the inferior parietal gyrus and the angular gyrus and lies inferior to the superior parietal gyrus. The rostral and caudal boundaries were the supramarginal gyrus and the parieto-occipital incisure respectively. The medial and lateral boundaries were the superior parietal gyrus and the middle temporal gyrus respectively (Christine Fennema-Notestine).
The part of the lateral ventricle extending downward and anteriorly in the temporal lobe.
Component of the occipital lobe. The rostral boundary was the first coronal slice above the calcarine sulcus where the cuneus cortex becomes visible whereas the caudal boundary was the last slice where the calcarine sulcus was visualized. The medial boundary was the most medial portion of the occipital and parietal cortices. The superio-lateral boundary was the parieto-occipital fissure whereas the inferolateral boundary was the pericalcarine cortex (Christine Fennema-Notestine).
Component of the pareital lobe. The rostral boundary was the posterior extent of the paracentral lobule whereas the caudal boundary was the lingual gyrus. The medial and lateral boundaries were the parieto-occipital fissure and the superior parietal gyrus respectively (Christine Fennema-Notestine).
medial area of the superior parietal cortex
Copmonent of the parietal lobe. The rostral and caudal boundaries of the superior parietal cortex were the precentral gyrus and lateral occipital cortex respectively. The medial and lateral boundaries were the precuneus and/or cuneus cortex and the infererior parietal cortex respectively (Christine Fennema-Notestine).
A subdivision of the cytoarchitecturally defined temporal region of cerebral cortex. It occupies the anterior transverse temporal gyrus (H) in the bank of the lateral sulcus on the dorsal surface of the temporal lobe. Cytoarchitecturally it is bounded medially by the parainsular area 52 (H) and laterally by the posterior transverse temporal area 42 (H) (Brodmann-1909). Adapted from Brain Info
Brodmann area 41, anterior transverse temporal
A subdivision of the cytoarchitecturally defined temporal region of cerebral cortex. It is located in the bank of the lateral sulcus on the dorsal surface of the temporal lobe. Cytoarchitecturally it is bounded medially by the anterior transverse temporal area 41(H) and laterally by the superior temporal area 22 (Brodmann-1909). Adapted from Brain Info
Brodmann area 42, posterior transverse temporal
The deep nuclei of telencephalic origin found in the basal region of the forebrain
Brodmann found a cytoarchitecturally homologous area in the monkey (Cercopithecus), but it was so weakly developed that he omitted it from the cortical map of that species (Brodmann-1909).
A set of amygdalar nuclei comprising the lateral nucleus (LA), the basal nucleus (BA), and the accessory basal nuclei (ABN). These nuclei are bordered laterally by the external capsule and medially by the central amygdalar nucleus as well as the amygdalohippocampal area. This definition refers to the rat Basolateral nuclear complex.
pars basolateralis (Corpus amygdaloideum)
These structures are referred to as nuclei but have a layered cortical like structure. These areas include the anterior amygdaloid area, posterior amygdaloid area, the periamygdaloid cortex, and the bed nucleus of the accessory olfactory tract.
pars corticomedialis (Corpus amygdaloideum)
corpus amygdaloideum pars corticomedialis
Component of the occipital lobe. The rostral and caudal boundaries of the lateral occipital cortex were the superior parietal gyrus and as the last visible portion of occipital cortex respectively. The medial and lateral boundaries were the cuneus/pericalcarine cortex and the inferior temporal/inferior parietal gyri respectively (Christine Fennema-Notestine).
Part of fornix adjacent to the fimbria comprising flattened bands of fibers that extend from the fimbria, running underneath the corpus callosum
Fibers of the accessory nerve (11th cranial nerve) contained within the medulla
Cytoarchitectural part of spinal cord gray matter
A group of cells ventral to the nucleus of brachium of inferior colliculus in the mouse (Paxinos-2001).
Candidate definition (refers specifically to mouse): "A group of cells ventral to the nucleus of brachium of inferior colliculus in the mouse (Paxinos-2001)." [NIFSTD:nlx_anat_1005003]
Layer of the superior colliculus, lying just deep to the outermost stratum zonale (Carpenter, A Core Text of Neuroanatomy, 3rd ed., 1985, pg 175)
stratum griseum superficiale colliculi superioris
stratum griseum superficiale of superior colliculus
superficial gray layer of superior colliculus
superficial grey layer of superior colliculus
superior colliculus superficial gray layer
superficial gray layer of the superior colliculus
superficial grey layer of the superior colliculus
lobulus parafloccularis dorsalis [h viii b]
Made obsolete as it grouped two unrelated classes
Horizontal limb of the diagonal band of Broca
nucleus of the horizontal limb of the diagonal band
Vertical limb of the diagonal band of Broca
nucleus of the vertical limb of the diagonal band
A funiculus of neuraxis that is part of a spinal cord.
The cerebrospinal nerves consist of numerous nerve fibers collected together and enclosed in membranous sheaths. A small bundle of fibers, enclosed in a tubular sheath, is called a funiculus; if the nerve is of small size, it may consist only of a single funiculus; but if large, the funiculi are collected together into larger bundles or fasciculi, which are bound together in a common membranous investment. Examples include: Anterior funiculus of the spinal cord Lateral funiculus of the spinal cord Posterior funiculus of the spinal cord Funiculus solitarius of the medulla Funiculus separans
A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system.
Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH)
consider adding link to UBERON:0002316 ! white matter of neuraxis
http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract, http://en.wikipedia.org/wiki/Myelin#Invertebrate_myelin
The proper palmar digital arteries travel along the sides of the phalanges (along the contiguous sides of the index, middle, ring, and little fingers), each artery lying just below its corresponding digital nerve. Alternative names for these arteries are: proper volar digital arteries, collateral digital arteries, arteriae digitales palmares propriae, or aa. digitales volares propriae. They anastomose freely in the subcutaneous tissue of the finger tips and by smaller branches near the interphalangeal joints. Each also gives off a couple of dorsal branches which anastomose with the dorsal digital arteries, and supply the soft parts on the back of the second and third phalanges, including the matrix of the fingernail. The proper palmar digital artery for the medial side of the little finger arises directly from the ulnar artery deep to the palmaris brevis muscle, but the rest arise from the common palmar digital arteries.
The plantar digital veins arise from plexuses on the plantar surfaces of the digits, and, after sending intercapitular veins to join the dorsal digital veins, unite to form four metatarsal veins.
The palmar digital veins (or volar digital veins) on each finger are connected to the dorsal digital veins by oblique intercapitular veins. Some sources distinguish between the 'proper palmar digital veins', which are more distal, and the 'common palmar digital veins', which are more proximal.
The dorsal digital arteries of foot are small arteries which supply the toes.
Dorsal digital arteries arise from the bifurcation of dorsal metacarpal arteries. They travel along the sides and dorsal aspects of the phalanges of the middle finger, ring finger, and little finger. They communicate with the proper palmar digital arteries. They run with the dorsal digital nerves of ulnar nerve and dorsal digital nerves of radial nerve.
Note Wikipedia article refers to manual dorsal digital artery
median dorsal digital artery for digit 01
median dorsal digital artery for digit I
median dorsal digital artery for digit 1
lateral dorsal digital artery for digit 05
lateral dorsal digital artery for digit V
lateral dorsal digital artery for digit 5
The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue.
A hollowed out area on the medial margin of the kidney. The renal sinus opens at the renal hilum; it contains the renal aa. and vv., major calyces and renal pelvis, perirenal fat
The rectal diverticulum is an outgrowth of the cloaca and links the pronephric kidney to the exterior
A pronephric nephron tubule is an epithelial tube that is part of the pronephros
The pronephric sinus is an ill-defined capillary network that lies between the pronephric tubules
TODO - check relationship to renal sinus, improve definition
The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus
The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros
The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule
The mesonephric proximal tubule extends from the capsule to the distal tubule
A renal sinus that is part of a right kidney.
A renal sinus that is part of a left kidney.
A renal sinus that is part of a mesonephros.
TODO - check relationship to renal sinus, add definition
In humans this refers to either the anterior or posterior auricular vein, passing in front of or behind the ear. This class also groups other auricular veins, including the greater, ventral, central auricular nerves. These may exhibit different branching structures. In the pig, the external jugular branches to the maxillary to the caudal auricular to the middle auricular, then onto various unique patterns
The highest intercostal artery (supreme intercostal artery, superior intercostal artery) is an artery in the human body that usually gives rise to the first and second posterior intercostal arteries, which supply blood to their corresponding intercostal space. It usually arises from the costocervical trunk, which is a branch of the subclavian artery.
dorsal branch of superior intercostal artery
classes unified on basis of spatial anatomy ontology synonyms
The posterior auricular vein begins upon the side of the head, in a plexus which communicates with the tributaries of the occipital vein and superficial temporal veins. It descends behind the auricula, and joins the posterior division of the posterior facial vein to form the external jugular. It receive the stylomastoid vein, and some tributaries from the cranial surface of the auricula.
Was obsoleted as it grouped a lip structure with an unknown MA vein, which be a genital vein
A band running from the pubic tubercle to the anterior superior iliac spine. Its anatomy is very important for operating on hernia patients. It forms the base of the inguinal canal through which an indirect inguinal hernia may develop. The inguinal ligament runs from the anterior superior iliac spine of the ilium to the pubic tubercle of the pubic bone. It is formed by the external abdominal oblique aponeurosis and is continuous with the fascia lata of the thigh.
an extension of the lacunar ligament that runs on the pectineal line of the pubic bone.
we include a disjointness axiom to avoid confusion that may arise from the synonyms 'ligamentum pectineale' and 'ligamentum pectinum' (eye trabecular meshwork)
Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP].
The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions.
A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head.
A basioccipital endochondral element that is composed primarily of a cartilage tissue.
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
depression at base of developing heart that contains a population of cardiomyocytes that migrate and contribute to the interventricular septum
A cartilaginous condensation that has_potential_to_develop_into a carpal bone.
A pre-cartilage condensation that has_potential_to_develop_into a carpal bone.
the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system
The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]
dorsal part of alar plate of metencephalon
A temporary depression caudal to the second pharyngeal arch, containing the succeeding pharyngeal arches; it is overgrown by the second pharyngeal arch and closes off as the cervical vesicle. This sinus is bounded in front by the hyoid arch, and behind by the thoracic wall.
it is ultimately obliterated by the fusion of its walls.
The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.
A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]
In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]
diencephalic part of interventricular foramen
A multi-tissue structure that has_potential_to_develop_into a diencephalon.
An outgrowth of the otic vesicle that forms the endolymphatic duct and sac during embryonic development. [TFD][VHOG]
consider obsoleting, the ethmoid is endochondral?
A exoccipital endochondral element that is composed primarily of a pre-cartilage condensation.
check this for developmental relationships
facio-acoustic VII-VIII preganglion complex
A differentiated genital tubercle that is part of a female reproductive system.
A femur endochondral element that is composed primarily of a pre-cartilage condensation.
An anatomical junctions that overlaps the foregut and midgut.
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
A tendon that has_potential_to_develop_into a central tendon.
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.
cranial derivative of septum transversum
A presumptive structure that has_potential_to_develop_into a forebrain.
TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)
A humerus endochondral element that is composed primarily of a cartilage tissue.
A humerus endochondral element that is composed primarily of a pre-cartilage condensation.
A iliac endochondral element that is composed primarily of a pre-cartilage condensation.
A incus endochondral element that is composed primarily of a pre-cartilage condensation.
in EHDAA2 this develops from both mandibular and maxillary mesenchyme. We have still to extend homology relationships from quadrate/incus to their ontogenic precursors (
A funnel-shaped diverticulum that extends downward from the anterior aspect of the floor of the third ventricle into the infundibulum of the hypophysis; the embryonic structure gives rise the neural component of the pituitary (pas nervosa).
in FMA this is a cavity, whereas in EHDAA2 it is an epithelial sac
The space separating the outer pigment epithelium and the inner neural retina of the optic cup and of the retina
The space separating the outer pigment epithelium and the inner neural retina of the optic cup and of the retina. [TFD][VHOG]
A ischial endochondral element that is composed primarily of a cartilage tissue.
A ischial endochondral element that is composed primarily of a pre-cartilage condensation.
A groove in the floor of the pharynx formed from the ventral diverticulum of endoderm that arises from the floor of the foregut caudal to the pharynx. This structure is the precursor for the larynx and trachea[WP,edited].
Note we currently have pharynx as part of the upper respiratory tract - separate by development?
Lung development begins with the appearance of the laryngotracheal groove, which is a small diverticulum that arises from the floor of the primitive pharynx at E9 in mouse and 4 wk in human.[well established][VHOG]
A pitlike depression in the ectoderm of the lens placode where the primordial lens is developing[TFD].
A pitlike depression in the ectoderm of the lens placode where the primordial lens is developing. [TFD][VHOG]
Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG]
the collection consisting of the two lateral swellings and the medial swelling
A differentiated genital tubercle that is part of a male reproductive system.
A malleus endochondral element that is composed primarily of a pre-cartilage condensation.
NC contributes in EHDAA2. editor note: TODO use EHDAA2 structure
Meckel's cartilage pre-cartilage condensation
An anatomical junctions that overlaps the mouth and foregut.
Trophectoderm that surrounds blastocyst cavity.
The part of the trophectoderm which surrounds the blastocoelic cavity. [See_Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.10][VHOG]
Groove between maxillary prominence and lateral nasal process.
On the nasal surface of the body of the maxilla, in front of the opening of the sinus is a deep groove, the lacrimal groove (or lacrimal sulcus), which is converted into the nasolacrimal canal, by the lacrimal bone and inferior nasal concha; this canal opens into the inferior meatus of the nose and transmits the nasolacrimal duct[WP] See also: oblique facial cleft
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
A small indentation in the central part of the optic placode.
A small indentation in the central part of the optic placode. [157-169, Mueller_F_and_ObRahilly_R, The_first_appearance_of_the_neural_tube_and_optic_primordium_in_the_human_embryo_at_stage_10._Anatomy_and_Embryology_(1985)_172][VHOG]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles (reference 1); The first morphological sign of eye development in vertebrates is the bilateral evagination of diencephalon in the early neurula. In mammals, this is marked by the appearance of the optic pit, whereas in fish and amphibians a bulging of the optic primordia is observed. Continued evagination of the optic primordia leads to the formation of the optic vesicles (reference 2).[well established][VHOG]
the pit deepens to form the optic vesicle.
Either of two openings transmitting nerves and blood vessels to or from the orbit.
In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity
the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles
A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG]
Each of the canals that connects the pericardial cavity with the peritoneal cavity and becomes a pleural cavity.
Each of the folds that grow out from the lateral part of the body wall. They fuse and meet with the dorsal and ventral mesentery of the foregut, separating the pleural cavities from the pericardial cavity.
As the folds grow towards the midline, carrying the phrenic nerve, the root of the folds migrate ventrally
Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity.
Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN10:0124020607][VHOG]
Trophectoderm that surrounds the inner cell mass (ICM).
The part of the trophectoderm overlying the inner cell mass. [See_Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.10][VHOG]
unlike mural trophectoderm cells which stop proliferating and become large polyploid cells (the primary trophoblastic giant cells) by endoreduplication, polar trophectoderm cells remain diploid, continue to proliferate and give rise to both the ectoplacental cone and the extraembryonic ectoderm[MP]
was obsoleted as it had no definition and the name was unclear. May refer to part of inferior vena cava or pre-hepatic portal vein FMA:71904
early vein that gives rise to various sinuses
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
presumptive cardiac ventricle heart tube
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle
A pubic endochondral element that is composed primarily of a pre-cartilage condensation.
A cartilaginous condensation that has_potential_to_develop_into a radius bone.
A radius-ulna endochondral element that is composed primarily of a pre-cartilage condensation.
EMAPA has a separate radius-ulna cartilage condensation.
A rib endochondral element that is composed primarily of a cartilage tissue.
A rib endochondral element that is composed primarily of a pre-cartilage condensation.
A scapula endochondral element that is composed primarily of a cartilage tissue.
A scapula endochondral element that is composed primarily of a pre-cartilage condensation.
the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005).
this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness
A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP].
check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme
A stapes endochondral element that is composed primarily of a pre-cartilage condensation.
independent of the mesenchymal condensation that will form the otic capsule
sternebral bone pre-cartilage condensation
A vein in the mammalian embryo or the adult of some lower vertebrates that is located on each side of the abdominal region ventromedial to the mesonephros and that in mammals participates in the formation of the inferior vena cava and the renal vein
A primordium that has_potential_to_develop_into a sublingual gland.
A primordium that has_potential_to_develop_into a submandibular gland.
Either of two veins in the mammalian embryo and various adult lower vertebrate forms located in the thoracic and abdominal regions dorsolateral to and on either side of the descending aorta and giving rise to the azygos and hemiazygos veins and a part of the inferior vena cava[MW]. These veins drain the body wall via the segmental intercostal veins, thus taking over the function of the posterior cardinals[ISBN]
telencephalic part of interventricular foramen
An extensive capillary network, spreading over the posterior and lateral surfaces of the lens of the eye. It disappears shortly after birth.
Soon after it forms, the mammalian lens becomes invested with a network of capillaries. (...) The capillary network on the posterior of the lens is the tunica vasculosa lentis (TVL).[well established][VHOG]
A cartilaginous condensation that has_potential_to_develop_into a ulna.
Ventral part of the cloacal membrane separating the gut from the fetus external environment. [TFD][VHOG]
During the 7th week the urorectal septum divides the cloacal membrane into a urogenital membrane (ventrally) and an anal membrane (dorsally) [http://www.embryology.ch/anglais/ugenital/genitexterne01.html]
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
An orbitalis muscle is a rudimentary nonstriated muscle (smooth muscle) that crosses from the infraorbital groove and sphenomaxillary fissure and intimately united with the periosteum of the orbit. It is often called Muller's muscle. One characteristic of Horner's Syndrome is enophthalmos (retraction of the eyeball into the orbit due to paralysis of the orbitalis muscle that spans the inferior orbital fissure). Its function is eyeball protrusion.
thin, narrow muscle placed near the anterior margin of the floor of the orbit.
Taxon notes (via VHOG): "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.331
The superior oblique muscle, or obliquus oculi superior, is a fusiform muscle in the upper, medial side of the orbit whose primary action is downward, lateral rotation of the eye. One of the extraocular muscles, the superior oblique is the only muscle innervated by the trochlear nerve (the fourth cranial nerve).
Cranial nerve IV innervated; dorsal in the obliquus group.[AAO]
A muscle in the orbit that depresses, adducts, and helps extort (rotate laterally) the eye. The inferior rectus muscle is the only muscle that is capable of depressing the pupil when it is in a fully abducted position.
The superior rectus muscle is a muscle in the orbit. It is one of the extraocular muscles. It is innervated by the superior division of the oculomotor nerve (Cranial Nerve III). In the primary position (looking straight ahead), the superior rectus muscle's primary function is elevation, although it also contributes to intorsion and adduction.
The superior pharyngeal constrictor muscle is a quadrilateral muscle, thinner and paler than the inferior pharyngeal constrictor muscle and middle pharyngeal constrictor muscle. [WP,unvetted].
The superior constrictor is a muscle that is an integral part of the pharyngeal tube that is attached to the mandible, pterygomandibular raphe, basioccipital bone, pterygoid process and midline raphe and is innervated by Cranial Nerve X via the pharyngeal plexus.[FEED]
the small glands located near the apex of the tongue on either side of the frenulum
A nucleus of brain that is part of a brainstem.
An embryonic cartilaginous frame, the nasal capsule, an evolutionary-conserved structure composed of ventral and dorsal components: the mesethmoid and ectethmoid cartilages, respectively.[PMID].
consider splitting this class. Developing cartilage in mammals?
Multi-tissue structure that is the connective tissue sheath that surrounds, except for external opening(s) in adult, the olfactory epithelium.[TAO]
Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium.[AAO]
Development information from Brian Hall, Bones and Cartilage: Developmental Skeletal Biology.[TAO]
In Aves: The nasal capsule is dorsoventrally divided into two parts: the upper part, the ectethmoid, serves olfaction and is composed of the lamina cribosa, the crista galli apophysis and the conchae. The lower part, the mesethmoid, is a thick cartilage bar extending from the corpus sphenoidalis to the rostral extremity of the nose (Fig. 1A-B). In the avian embryo, the mesethmoid constitutes the cartilage primordium of the upper beak.
In avians, the mesethmoid supports upper beak formation, whereas the ectethmoid comprises elements of the olfactory system, including the lamina cribosa, the crista galli apophysis and the conchae.
In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates
Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase]
Surface structure that is the region of the head in front of and between the orbits, and above the lower jaw. Nares are located on the snout[ZFA].
One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.
relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO]
Portion of the renal tubule which is just posterior to the proximal straight tubule.
Portion of the pronephric tubule that is immediately posterior to the late proximal tubule.[AAO]
in XAO this is pronephric; in ZFA it is an adult structure. we treat it here as generic. consider placing XAO under proneprhic subclass. check relationship with EDCT.
early distal tubule of capillary loop nephron
A choroid plexus stroma that is part of a lateral ventricle.
definitions should be fixed to use generic stroma class
A choroid plexus stroma that is part of a third ventricle.
A choroid plexus stroma that is part of a fourth ventricle.
A peritubular capillary that is part of a outer medulla of kidney.
kidney outer medulla peritubular capillary
outer renal medulla peritubular capillary
Compare with lesser sac / omental bursa and its cavities / recesses
The hepatorenal recess or subhepatic recess is the space that separates the liver from the right kidney. As a potential space, the recess is not filled with fluid under normal conditions. However, fluid can collect in this space in circumstances where the abdomen fills with fluid, such as hemoperitoneum. This fluid may be seen on ultrasound or computed tomography (CT scan).
recessus hepatorenalis recessi subhepatici
A small artery that passes through the ring of the stapes; while the stapedial artery is a temporary artery thought to disappear at late embryonic stage in humans, the mouse stapedial artery is complete by E13 and persists into adulthood[MP].
An artery that connects two larger arteries.
An external iliac artery branch that supplies blood to the anterior abdominal wall.
A prinicipal vein of limb that is part of a forelimb.
A prinicipal vein of limb that is part of a hindlimb.
Either of two veins including the inferior and superior epigastric veins.
The vasa hyaloidea propria and tunica vasculosa lentis are small branches of the hyaloid artery which fill the primary vitreous
The terminal end of the ureteric tree; the ureteric tip cells are proliferating immature cells located at the branching points that induce the adjacent cap mesenchyme to undergo nephrogenesis.
the part of the renal interstitium surrounding the pelvis
part of afferent arteriole forming juxtaglomerular complex
part of afferent arteriole forming the juxtaglomerular complex
distal straight tubule premacula segment
kidney medulla loop of Henle ascending limb thick segment
medullary thick ascending limb of Henle's loop
renal medulla loop of Henle ascending limb thick segment
premacula segment of distal straight tubule
A specialized hair usually employed for tactile sensation. Vibrissae hair grow around the nostrils, above the lips, and on other parts of the face of most mammals, and all primates except humans. vibrissae are different from other hairs because they are implanted in a special hair follicle incorporating a capsule of blood called a blood sinus and heavily innervated by sensory nerves[WP].
In harbor seals, the structure of the vibrissal shaft is undulated (wavy) and flattened. This specialization is also found in most true seals. In contrast, the whiskers of the California sea lion are circular or elliptical in cross-section and are smooth.
part of the base of the cranium between the basioccipital and the presphenoid, which usually ossifies separately in the embryo or in the young, and becomes a part of the sphenoid in the adult; in many animals it persists as a separate bone between the basioccipital bone and the presphenoidal bone
An endochondral bone that is located ventral to the pterosphenoid and dorsal to the parasphenoid. Basisphenoid is a median bone that is usually Y-shaped.[TAO]
Endochondral ossification of the ventromedial portion of the braincase.[AAO]
"Endochondral ossification of the ventromedial portion of the braincase." [AAO:0000040] // "An endochondral bone that is located ventral to the pterosphenoid and dorsal to the parasphenoid. Basisphenoid is a median bone that is usually Y-shaped." [TAO:0000169]
A costal cartilage that is part of a xiphoid process.
Distal, cartilaginous portion of the sternum.[AAO]
A bone tissue that is part of a xiphoid process.
the unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species
found in most mammals, with the exception of humans
The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans;it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals
A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart).
Component of the middle frontal gyrus. The rostral boundary of the middle frontal gyrus was the rostral extent of the middle frontal gyrus whereas the caudal boundary was the precentral gyrus. The medial and lateral boundaries were designated as the superior frontal sulcus and the inferior frontal sulcus respectively (Christine Fennema-Notestine).
Component of the middle frontal gyrus The rostral boundary is the first appearance of the superior frontal sulcus whereas the caudal boundary is the middle frontal gyrus. The medial and lateral boundaries are the superior frontal sulcus and the inferior frontal sulcus respectively (Christine Fennema-Notestine).
Brodmann area 5 is one of Brodmann's cytologically defined regions of the brain. It is involved in somatosensory processing and association.
Brodmann area 6, or BA6, is part of the frontal cortex in the human brain. Situated just anterior to the primary motor cortex, it is composed of the premotor cortex and, medially, the supplementary motor area, or SMA. This large area of the frontal cortex is believed to play a role in the planning of complex, coordinated movements. Brodmann area 6 is also called agranular frontal area 6 in humans because it lacks an internal granular cortical layer (layer IV). It is a subdivision of the cytoarchitecturally defined precentral region of cerebral cortex. In the human brain, it is located on the portions of the precentral gyrus that are not occupied by the gigantopyramidal area 4; furthermore, BA6 extends onto the caudal portions of the superior frontal and middle frontal gyri. It extends from the cingulate sulcus on the medial aspect of the hemisphere to the lateral sulcus on the lateral aspect. It is bounded rostrally by the granular frontal region and caudally by the gigantopyramidal area 4 (Brodmann, 1909).
Brodmann area 30, also known as agranular retrolimbic area 30, is a subdivision of the cytoarchitecturally defined retrosplenial region of the cerebral cortex. In the human it is located in the isthmus of cingulate gyrus. Cytoarchitecturally it is bounded internally by the granular retrolimbic area 29, dorsally by the ventral posterior cingulate area 23 and ventrolaterally by the ectorhinal area 36 (Brodmann-1909).
Brodmann area 31, also known as dorsal posterior cingulate area 31, is a subdivision of the cytoarchitecturally defined cingulate region of the cerebral cortex. In the human it occupies portions of the posterior cingulate gyrus and medial aspect of the parietal lobe. Approximate boundaries are the cingulate sulcus dorsally and the parieto-occipital sulcus caudally. It partially surrounds the subparietal sulcus, the ventral continuation of the cingulate sulcus in the parietal lobe. Cytoarchitecturally it is bounded rostrally by the ventral anterior cingulate area 24, ventrally by the ventral posterior cingulate area 23, dorsally by the gigantopyramidal area 4 and preparietal area 5 and caudally by the superior parietal area 7 (H) (Brodmann-1909).
Brodmann area 31, dorsal posterior cingulate
Brodmann area 33, also known as pregenual area 33, is a subdivision of the cytoarchitecturally defined cingulate region of cerebral cortex. It is a narrow band located in the anterior cingulate gyrus adjacent to the supracallosal gyrus in the depth of the callosal sulcus, near the genu of the corpus callosum. Cytoarchitecturally it is bounded by the ventral anterior cingulate area 24 and the supracallosal gyrus (Brodmann-1909).
Brodmann area 34 is a part of the brain. It has been described as part of the entorhinal area. It has been described as part of the superior temporal gyrus.
Brodmann area 37, or BA37, is part of the temporal cortex in the human brain. This area is known as occipitotemporal area 37 (H). It is a subdivision of the cytoarchitecturally defined temporal region of cerebral cortex. It is located primarily in the caudal portions of the fusiform gyrus and inferior temporal gyrus on the mediobasal and lateral surfaces at the caudal extreme of the temporal lobe. Cytoarchitecturally it is bounded caudally by the peristriate Brodmann area 19, rostrally by the inferior temporal area 20 and middle temporal area 21 and dorsally on the lateral aspect of the hemisphere by the angular area 39 (H) (Brodmann-1909).
Part of the cytoarchitecturally defined frontal region of cerebral cortex. In the human, it occupies the triangular part of the inferior frontal gyrus (human) and, surrounding the anterior horizontal limb of the lateral sulcus (human), a portion of the orbital part of the inferior frontal gyrus (human). Bounded caudally by the anterior ascending limb of the lateral sulcus (human), it borders on the insula in the depth of the lateral sulcus. Cytoarchitectonically it is bounded caudally by the opercular area 44, rostrodorsally by the area 46 of Brodmann (human) and ventrally by the area 47 of Brodmann (human) (Brodmann-1909) (Adapted from Brain Info)
Brodmann area 45 (BA45), is part of the frontal cortex in the human brain. Situated on the lateral surface, inferior to BA9 and adjacent to BA46. This area is also known as pars triangular (of the inferior frontal gyrus). In the human, it occupies the triangular part of inferior frontal gyrus (H) and, surrounding the anterior horizontal limb of lateral sulcus (H), a portion of the orbital part of inferior frontal gyrus (H). Bounded caudally by the anterior ascending limb of lateral sulcus (H), it borders on the insula in the depth of the lateral sulcus. In terms of cytoarchitecture, it is bounded caudally by the opercular area 44 (BA44), rostrodorsally by the middle frontal area 46 (BA46), and ventrally by the orbital area 47 (BA47) (Brodmann-1909)[Wikipedia:Brodmann_area_45].
Brodmann area 46, or BA46, is part of the frontal cortex in the human brain. It is between BA10 and BA45. BA46 is known as middle frontal area 46. In the human it occupies approximately the middle third of the middle frontal gyrus and the most rostral portion of the inferior frontal gyrus. Brodmann area 46 roughly corresponds with the dorsolateral prefrontal cortex (DLPFC), although the borders of area 46 are based on cytoarchitecture rather than function. The DLPFC also encompasses part of granular frontal area 9, directly adjacent on the dorsal surface of the cortex. Cytoarchitecturally, BA46 is bounded dorsally by the granular frontal area 9, rostroventrally by the frontopolar area 10 and caudally by the triangular area 45 (Brodmann-1909). There is some discrepancy between the extent of BA8 (Brodmann-1905) and the same area as described by Walker (1940)
Brodmann area 47, or BA47, is part of the frontal cortex in the human brain. Curving from the lateral surface of the frontal lobe into the ventral (orbital) frontal cortex. It is below areas BA10 and BA45, and beside BA11. This area is also known as orbital area 47. In the human, on the orbital surface it surrounds the caudal portion of the orbital sulcus (H) from which it extends laterally into the orbital part of inferior frontal gyrus (H). Cytoarchitectonically it is bounded caudally by the triangular area 45, medially by the prefrontal area 11 of Brodmann-1909, and rostrally by the frontopolar area 10 (Brodmann-1909). It incorporates the region that Brodmann identified as 'Area 12' in the monkey, and therefore, following the suggestion of Michael Petrides, some contemporary neuroscientists refer to the region as 'BA47/12. ' BA47 has been implicated in the processing of syntax in spoken and signed languages, and more recently in musical syntax.
Retrosubicular area 48 is a subdivision of the cytoarchitecturally defined hippocampal region of the cerebral cortex. In the human it is located on the medial surface of the temporal lobe. Cytoarchitectually it is bounded rostrally by the perirhinal area 35 and medially by the presubiculum. While described by Brodmann (Brodmann-1909), it was not included in his areal maps of human cortex (Brodmann-1909; Brodmann-1910).
hadjikhani et al. (1998) visuotopic area v2d
osseous part of external acoustic meatus
An interosseous muscle that is part of a pes.
Interroseous muscles are short digital muscles found together on the plantar aspect of the hindlimb. They act as shock absorbers for the pes, and closely resemble the interossei found in the forelimb. They originate from the proximal ends of all metatarsal bones and initially insert on the sesamoid bones at the metatarsophalangeal joints. The interosseous are then continued by distal sesamoidean ligaments which join the extensor tendons and attach to the phalanges[MURDOCH:920].
In human anatomy, the dorsal interossei of the foot are four muscles situated between the metatarsal bones.
The plantar interossei, three in number, lie beneath rather than between the metatarsal bones, and each is connected with but one metatarsal bone. They arise from the bases and medial sides of the bodies of the third, fourth, and fifth metatarsal bones, and are inserted into the medial sides of the bases of the first phalanges of the same toes, and into the aponeuroses of the tendons of the Extensor digitorum longus.
The palmar interossei (interossei volares) are small muscles in the hand that lie on the anterior aspect of the metacarpals. They are smaller than the dorsal interossei of the hand, which lie between the metacarpals
Part of what are called the basal ganglia of the brain which consist of the globus pallidus and the ventral pallidum.
The term dorsal pallidum refers to the predominant portion of the globus pallidus in the striatopallidal system, which is defined by connectivity and neurochemical staining. The dorsal pallidum is distinguished from the ventral pallidum by a boundary that is partially defined by the anterior commissure. The remainder of the boundary is indistinct in sections stained for Nissl substance ( Heimer-1995 )
Recesses of the kidney pelvis which divides into two wide, cup-shaped major renal calices, with each major calix subdivided into 7 to 14 minor calices. Urine empties into a minor calix from collecting tubules, then passes through the major calix, renal pelvis, and ureter to enter the urinary bladder. (From Moore, Clinically Oriented Anatomy, 3d ed, p211)
A lobe of lung that is part of a right lung.
4 in mice, divided into 3 in human by two interlobal fissures
System pertaining to a bronchus and alveoli.
The fluid portion of the semen, in which the spermatozoa are suspended[BTO].
this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted)
we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid
This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation
seminal fluid may have a role in sperm capacitation, sperm motility
The muscles that move the eye. Included in this group are the medial rectus, lateral rectus, superior rectus, inferior rectus, inferior oblique, superior oblique, musculus orbitalis, and levator palpebrae superioris.
we follow MA in making this a subclass of extra-ocular muscle but the distinction is not clear
Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble.
A portion of organism substance that secreted_by a zone of skin.
A portion of organism substance that secreted_by a male reproductive system.
male reproductive system fluid/secretion
A portion of organism substance that secreted_by a female reproductive system.
female reproductive system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
A fluid that is secreted by a mammary gland.
A loop of Henle that is part of a kidney outer medulla inner stripe.
outer medulla inner stripe loop of henle
A loop of Henle that is part of a kidney outer medulla outer stripe.
outer medulla outer stripe loop of henle
A tube in the kidney that collect and transport urine.
in ZFA this is defined as part of mesonephros
Obsoleted because this ontology discusses part-wise grouping classes
A tube that is part of a excretory system.
in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]
A urethral meatus that is part of a female urethra[Automatically generated definition].
The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts.
ostium urethrae externum (urethra feminina)
Myocardium of ventricle which is continuous with the tunica media of aorta.[FMA]
Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk.[FMA]
A nucleus of brain that is part of a hypothalamus.
A nucleus of brain that is part of a diencephalon.
A trabecula carnea that is part of a heart right ventricle.
A trabecula carnea that is part of a heart left ventricle.
trabeculae carneae (ventriculus sinister)
The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:
FMA also has FMA:29321 but it's not clear how this differs
A fold or lobe or pair of lobes of the body wall of a mollusk or brachiopod that in shell-bearing forms lines the shell and bears shell-secreting glands.
Within the shell is a fleshy layer of tissue called the mantle; there is a cavity (the mantle cavity) between the mantle and the body wall proper.
A muscle organ that is part of a mantle.
Acellular mineralized structure located in the statocyst (balance organ) of some aquatic invertebrates[WP,CJM].
A balance sensory receptor present in some aquatic invertebrates[WP].
An organ that is part of a vestibular system.
Transduate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph).
Fluids found within the osseous labyrinth (PERILYMPH) and the membranous labyrinth (ENDOLYMPH) of the inner ear. (From Gray's Anatomy, 30th American ed, p1328, 1332[MESH:A12.207.571])
The ligamentum venosum is the fibrous remnant of the ductus venosus of the fetal circulation. Usually, it is attached to the left branch of the portal vein within the porta hepatis (gateway to the liver). It may be continuous with the round ligament of liver (ligamentum teres hepatis). It is invested by the peritoneal folds of the lesser omentum within a fissure on the inferior surface of the liver between the caudate and main parts of the left lobe.
A degenerative string of tissue that exists in the free edge of the falciform ligament of the liver. Anatomically, the round ligament divides the left part of the liver into medial and lateral sections. The round ligament represents the remnant of the fetal left umbilical vein. The round ligament therefore only exists in mammals. Prenatally and for a month or two after birth, the left umbilical vein is patent, subsequently degenerating to fibrous tissue, the round ligament. The umbilical vein/round ligament inserts around the umbilicus and is an important landmark of the inner surface of the anterior abdominal wall[WP].
The round ligament of the uterus originates at the uterine horns, in the parametrium. It leaves the pelvis via the deep inguinal ring, passes through the inguinal canal and continues on to the labia majora where its fibers spread and mix with the tissue of the mons pubis[WP]. A fibromuscular band that attaches to the uterus and then passes along the broad ligament, out through the inguinal ring, and into the labium majus[MESH].
Anatomical structure which is a remnant of an embryonic structure in the postnatal period. Examples: median umbilical ligament, paroohoron, prostatic utricle, ligamentum arteriosum.[FMA]
A vestigial embryonic structure that develops_from a artery.
A vestigial embryonic structure that develops_from a vein.
The cranial, thin portion of the gubernaculum.
Attaches to mesonephric-gonadal complex[doi:10.1046/j.1469-7580.2002.00087.x]
Presumptive structure of the blastula that will develop into endoderm.
Ossified pars articularis of the palatoquadrate cartilage.
Endochondral bone that commonly articulates with the ectopterygoid anteriorly, the metapterygoid dorsally, and the symplectic postero-medially. The quadrate is formed from the posterior part of the palatoquadrate cartilage, or pars quadrata. The quadrate is a paired bone.[TAO]
relationship loss: overlaps quadrate-hyomandibula joint (TAO:0001801)[TAO]
relationship loss: overlaps quadrate-metapterygoid joint (TAO:0001803)[TAO]
The quadrate commonly has a triangular shape, with its lower vertex, or condyle, for articulation with the lower jaw, and an elongate postero-ventral or postero-dorsal elongate process. The presence of an elongate postero-ventral or postero-dorsal process is a synapomorphy of teleosts (Arratia and Schultze, 1990; Arratia, 1999).[TAO]
In snakes, the quadrate bone has become elongated and very mobile, and contributes greatly to their ability to swallow very large prey items. In mammals the articular and quadrate bones have migrated to the middle ear and are known as the malleus and incus.
Endochondral bone that commonly articulates with the ectopterygoid anteriorly, the metapterygoid dorsally, and the symplectic postero-medially. The quadrate is formed from the posterior part of the palatoquadrate cartilage, or pars quadrata. The quadrate is a paired bone.
Tissue is fated to develop into the hypochord.
Tissue along the lateral edges of the shield that is fated to develop into the hypochord[ZFA:curator].
Unlike in frogs and axolotl, the hypochord does not appear to be endodermally derived[ZFA]
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
Cranial cartilage which is bilaterally paired and develops as a dorsal plate-like projection of the anterolateral ethmoid plate, which are oriented perpendicular to the ethmoid plate. It fuses dorsally to the taenia marginalis anterior, and it joins the ethmoid cartilage medially.
In the larva, structure that is fused to the wall of the braincase, lateral to the olfactory foramen, and separates the nasal capsule and orbit. In the adult frog it constitutes the ventral part of postnasal wall.[AAO]
Unpaired thin dorsal sheet of cartilage that partially covers the posterior chondrocranium.
Roof between frontoparietal foramen and otic capsules, confluent with taenia tecti marginales.[AAO]
posterior tectum synoticum in humans - a skull roof element of the chondrocranium - temporarily exists in the territory of the interparietal during fetal life, and may be resposible for the sutura mendosa
In AAO the def is 'Roof between frontoparietal foramen and otic capsules, confluent with taenia tecti marginales.', In TAO/ZFA this gives rise to supraoccipital and sphenotic.
A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified].
this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints
Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO]
in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible
The medial umbilical ligament is a paired structure found in human anatomy. It is on the deep surface of the anterior abdominal wall, and is covered by the medial umbilical folds.
The corpus cavernosum clitoridis is one of a pair of sponge-like regions of erectile tissue which contain most of the blood in the clitoris during clitoral erection. This is homologous to the corpus cavernosum penis in the male; the body of the clitoris contains erectile tissue in a pair of corpora cavernosa (literally 'cave-like bodies'), with a recognisably similar structure.
White covering over one of: penis, testicles or ovaries.
Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans.
A rigid covering that envelops an object.
may be obsoleted after integumental system overhaul
Aponeuroses are layers of flat broad tendons. They have a shiny, whitish-silvery color, and are histologically similar to tendons, but are very sparingly supplied with blood vessels and nerves. When dissected, aponeuroses are papery, and peel off by sections. The primary regions with thick aponeurosis is in the ventral abdominal region, the dorsal lumbar region, and in the palmar region. Their primary function is to join muscles and the body parts the muscles act upon[Wikipedia:Aponeurosis].
in ZFA, aponeuroses are subtypes of tendons, but this is inconsistent with tendons being muscle-bone connections
A large vein or channel for the circulation of venous blood
An external ear that is in the right side of a multicellular organism.
An external ear that is in the left side of a multicellular organism.
A small conical pouch projections located on the upper anterior portion of each atrium of the heart.
A muscular pouch connected to the left atrium of the heart
A small conical muscular pouch attached to the right atrium of the heart.
A process of the scapula in most mammals reprsenting the remnant of the coracoid bone of lower vertebrates thas has become fused with the scapula.
The coracoid process is a small hook-like structure on the lateral edge of the superior anterior portion of the scapula. Pointing laterally forward, it, together with the acromion, serves to stabilize the shoulder joint. It is palpable in the deltopectoral groove between the deltoid and pectoralis major muscles. It is the site of attachment for several structures: * The pectoralis minor muscle - to 3rd to 5th ribs. * The short head of biceps brachii muscle - to Radial tuberosity. * The coracobrachialis muscle - to medial humerus. * The coracoclavicular ligament - to the clavicle. (The ligament is formed by the conoid ligament and trapezoid ligament.) * The coracoacromial ligament - to the acromion[WP][Wikipedia:Coracoid_process].
In humans is situated on its superior border and serves for the attachment of various muscles
The lingual veins begin on the dorsum, sides, and under surface of the tongue, and, passing backward along the course of the lingual artery, end in the internal jugular vein. The vena comitans of the hypoglossal nerve (ranine vein), a branch of considerable size, begins below the tip of the tongue, and may join the lingual; generally, however, it passes backward on the Hyoglossus, and joins the common facial.
Vein which collects blood from the tongue and drains into the external jugular vein.[AAO]
The lumbar arteries are in series with the intercostals. They are usually four in number on either side, and arise from the back of the aorta, opposite the bodies of the upper four lumbar vertebrC&. A fifth pair, small in size, is occasionally present: they arise from the middle sacral artery. They run lateralward and backward on the bodies of the lumbar vertebrC&, behind the sympathetic trunk, to the intervals between the adjacent transverse processes, and are then continued into the abdominal wall. The arteries of the right side pass behind the inferior vena cava, and the upper two on each side run behind the corresponding crus of the diaphragm. The arteries of both sides pass beneath the tendinous arches which give origin to the Psoas major, and are then continued behind this muscle and the lumbar plexus. They now cross the Quadratus lumborum, the upper three arteries running behind, the last usually in front of the muscle. At the lateral border of the Quadratus lumborum they pierce the posterior aponeurosis of the Transversus abdominis and are carried forward between this muscle and the Obliquus internus. They anastomose with the lower intercostal, the subcostal, the iliolumbar, the deep iliac circumflex, and the inferior epigastric arteries.
The celiac artery, also known as the celiac trunk, is the first major branch of the abdominal aorta. Branching from the aorta 'anterior to the upper part of T12' vertebra in humans, it is one of three anterior/ midline branches of the abdominal aorta.
The median umbilical ligament is a structure in human anatomy. It is a shrivelled piece of tissue that represents the remnant of the embryonic urachus. It extends from the apex of the bladder to the umbilicus, on the deep surface of the anterior abdominal wall. It is unpaired. It is covered by the median umbilical fold Lateral to this structure are the medial umbilical ligament (which is a different structure, not to be confused) and the lateral umbilical ligament.
the continuation of each corpus cavernosum of the penis, diverging posteriorly to be attached to the pubic arch.
The continuation of the clitoris on each side of the corpus cavernosum, diverging from the body posteriorly and attached to the pubic arch.
On the head of the epididymis is a small stalked appendage (sometimes duplicated). It is named the appendix of the epididymis (or pedunculated hydatid), and is usually regarded as a detached efferent duct. This structure is derived from the Wolffian duct as opposed to the appendix testis which is derived from the mullerian duct remnant.
A muscle layer that is part of a fallopian tube.
The Tunica Albuginea is the fibrous covering of the testis. It is a dense blue-white membrane, composed of bundles of white fibrous tissue which interlace in every direction. It is covered by the tunica vaginalis, except at the points of attachment of the epididymis to the testis, and along its posterior border, where the spermatic vessels enter the gland. It is applied to the tunica vasculosa over the glandular substance of the testis, and, at its posterior border, is reflected into the interior of the gland, forming an incomplete vertical septum, called the mediastinum testis (corpus Highmori).
The layer of connective tissue covering the testicles. [Wikipedia_(15/09/09)][VHOG]
The tunica albuginea testis is the major component of the capsule of mammalian testes. (...) Our results from studying the mole provide evidence that the spatio-temporal pattern of testis development is not perfectly conserved in mammals, since we found differences with respect to the mouse testis organogenesis. This fact is even more significant when we consider that, apart from the mouse, the mole is probably the one of the best-known mammalian species in terms of the genetic control of testis development, implying that more peculiarities would be found if more species were investigated.[uncertain][VHOG]
The tunica albuginea is the fibrous envelope of the corpora cavernosa penis. It is comprised of approximately 5% elastin, an extensible tissue that is primarily made up of the amino acids glycine, valine, alanine, and proline. The majority of the remaining tissue is comprised of collagen, which is made up of lysine, proline, glycine, alanine, and other amino acids . The tunica albuginea is directly involved in maintaining an erection; that is due to Buck's fascia constricting the deep dorsal vein of the penis, preventing blood from leaving and thus sustaining the erect state. The trabeculC& of the tunica albuginea are more delicate, nearly uniform in size, and the meshes between them smaller than in the corpora cavernosa penis: their long diameters, for the most part, corresponding with that of the penis. The external envelope or outer coat of the corpus spongiosum is formed partly of unstriped muscular fibers, and a layer of the same tissue immediately surrounds the canal of the urethra.
An adventitia that is part of a epididymis.
A muscle layer that is part of a epididymis.
An adventitia that is part of a vas deferens.
An adventitia that is part of a seminal vesicle.
A fold of peritoneum that extends out from the ovary to the wall of the pelvis.
Some sources consider it a part of the broad ligament of uterus[2] while other sources just consider it a "termination" of the ligament.[3]
The tunica vaginalis is the serous covering of the testis. It is a pouch of serous membrane, derived from the saccus vaginalis of the peritoneum, which in the fetus preceded the descent of the testis from the abdomen into the scrotum. After its descent, that portion of the pouch which extends from the abdominal inguinal ring to near the upper part of the gland becomes obliterated; the lower portion remains as a shut sac, which invests the surface of the testis, and is reflected on to the internal surface of the scrotum; hence it may be described as consisting of a visceral and a parietal lamina.
tunica vaginalis testis has two layers: visceral and parietal; the visceral layer lies on the anterolateral surface of the testis and epididymis; the parietal layer lines the inner surface of the scrotal sac
we follow FMA is classifying as membranous layer - but this does not account for relationship to mesolthelium (subclass or has part?). The FMA also has 'sac of tunica vaginalis', which is a serous sac.[FMA]
The appendix testis is a vestigial remnant of the Mullerian duct, present on the upper pole of the testis and attached to the tunica vaginalis. It is present about 90% of the time.
the label hydatid of morgagni is ambiguous w.r.t male vs female. The ncita structure 'hydatic of morgani' is male and thus belongs here.
a cystlike remnant of the müllerian duct on the upper end of the testis; corresponding female structure: one of the small pedunculated structures attached to the uterine tubes near their fimbriated end; remnants of the mesonephric ducts[http://medical-dictionary.thefreedictionary.com/].
See also 'vesicular appendage of epoophoron'. TODO: check vesicular appendages
A muscle tissue that is part of a vagina.
Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP].
The perineal body (or central tendon of perineum) is a pyramidal fibromuscular mass in the middle line of the perineum at the junction between the urogenital triangle and the anal triangle . It is found in both males and females. In males, it is found between the bulb of penis and the anus; in females, is found between the vagina and anus, and about 1.25 cm in front of the latter. The perineal body is essential for the integrity of the pelvic floor, particularly in females. Its rupture during delivery leads to widening of the gap between the anterior free borders of levator ani muscle of both sides, thus predisposing the woman to prolapse of the uterus, rectum, or even the urinary bladder.
Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure.
Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO]
The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans
FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself
A joint that connects one phalanx to another along a proximodistal axis.
Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint].
One of a pair of ligaments arranged like a letter X.[1] They occur in several joints of the body, such as the knee. In a fashion similar to the cords in a toy Jacob's ladder, the crossed ligaments stabilize the joint while allowing a very large range of motion[WP].
A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis.
currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)
An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO].
typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle.
The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance.
galea aponeurotica; aponeurosis epicranialis
The hemiazygos vein (vena azygos minor inferior) is a vein running superiorly in the lower thoracic region, just to the left side of the vertebral column.
The major anatomic variation between the pig and other mammalian species is the presence of the large left azygos vein, which enters the coronary sinus (Fig. 1). In other mammals, hemiazygos vein enters the pre- cava.
The greater palatine artery is a terminal branch of the maxillary artery. It branches off of the maxillary artery in the pterygopalatine fossa and descends through the greater palatine foramen along with the greater palatine nerve and supplies the hard palate. It also anastomosis through the incisive canal with the sphenopalatine artery to supply the nasal cavity.
TODO - check for synonymy between greater and major; branching_part_of relation is made in FMA at level of descending GPA
The accessory hemiazygos vein (vena azygos minor superior) is a vein on the left side of the vertebral column that generally drains the fifth through eighth intercostal spaces on the left side of the body[WP].
The great cerebral vein is one of the large blood vessels in the skull draining the cerebrum (brain)[WP,unvetted]
Anatomical cavity that is part of the sella turcica and contains the pituitary gland.
On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP].
The infratemporal surface of the maxilla is pierced about its center by the apertures of the alveolar canals, which transmit the posterior superior alveolar vessels and nerves[WP].
the three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers
In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]
A fat pad that is part of a orbital region.
Taxon notes notes: In domestic mammals the Ductus incisivus is considerably better developed than in man. It is not accommodated in a Canalis incisivus, as in man, but in the Fissura palatina[NOMINA ANATOMICA VETERINARIA (2005)]
A canal within the mandible that contains the inferior alveolar nerve, inferior alveolar artery, and inferior alveolar vein. It runs obliquely downward and forward in the ramus, and then horizontally forward in the body, where it is placed under the alveoli and communicates with them by small openings
TAO has mandibular sensory canal, which is part of the lateral line system
An entrance or exit of the inguinal canal
A the thin layer of smooth muscle found in most parts of the gastrointestinal tract, located outside the lamina propria mucosae and separating it from the submucosa[WP].
An anatomical boundary that adjacent_to a epithelium.
Second of the two openings to perforate the septum primum between the two atria of the embryonic heart. [TFD][VHOG]
The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether. [ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620]; [about heart development] In the various tetrapod classes ontogenetic events essentially recapitulate the phylogenetic stages.[well established][VHOG]
A cartilaginous ridge within the trachea that runs anteroposteriorly between the two primary bronchi at the site of the tracheal bifurcation at the lower end of the trachea.
A smooth muscle tissue that bridges the gap between free ends of C-shaped cartilages at the posterior border of the trachea, adjacent to the esophagus. A primary function of the trachealis is to constrict the windpipe, allowing for higher velocity of air in the windpipe during coughing[WP, modified].
The hypoglossal canal is a bony canal in the occipital bone of the skull.
A gap between bones in the skull at the junction of the sagittal suture and lambdoidal suture.
In humans it generally closes in 6–8 weeks from birth. A delay in closure is associated with congential hypothyroidism
A vein that is part of a vertebral column.
The sublingual caruncle is a site on either side of the frenulum linguae on the sublingual surface of the tongue. There it denotes the site at which the submandibular gland empties into the oral cavity.
A small fold of mucous membrane extending from the floor of the mouth to the midline of the underside of the tongue.
The tentorium cerebelli or cerebellar tentorium is an extension of the dura mater that separates the cerebellum from the inferior portion of the occipital lobes.
The tentorium cerebelli or cerebellar tentorium (Latin: [][VHOG]
A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes.
TODO - check neural vs vertebral canal; embryonic vs adult?
Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO]
An example of this is found in Caenorhabditis elegans
A vasculature that is part of a cerebellum.
The mammillary axonal complex is formed by the axons from the lateral, medial mammillary and the dorsal premammillary nuclei which share a branching pattern. Every neuron gives off one axonal stem that bifurcates into 2 branches. One of the branches is directed dorsally to the thalamus and another caudally to the midbrain[GO].
A fiber pathway that originates from neurons in the posterior hypothalamic region and projects to various nuclei of the anterior nuclear group of the thalamus. It is a composite structure that consists of the mammillothalamic tract of the hypothalamus and the mammillothalamic tract of the thalamus (Carpenter-1983). (from Brain Info.org)
The mammillothalamic tract is the collection of axons that connects the two major subdivisions of the diencephalon (hypothalamus and thalamus) and closes the diencephalic circuit[GO][GO:0061374].
The mammillothalamic fasciculus arises from cells in both the medial and lateral nuclei of the mammillary body and by fibers that are directly continued from the fornix. The Mammillothalamic fasciculus then connects the mammillary body to the dorsal tegmental nuclei, the ventral tegmental nuclei, and the anterior thalamic nucleus [WP]
The mammillotectal tract is the collection of axons that connects the ventral diencephalon to the superior colliculus.
The mammillotegmental tract is the collection of axons that connects the ventral diencephalon to the tegmentum and pons
The median pit on the dorsum of the posterior part of the tongue, from which the limbs of a V-shaped furrow run forward and outward; the foramen cecum is the point of attachment of the thyroglossal duct and is formed during the embryological descent of the thyroid gland
The frontal crest of the frontal bone ends below in a small notch which is converted into a foramen, the foramen cecum, by articulation with the ethmoid. This foramen varies in size in different subjects, and is frequently impervious; when open, it transmits a vein from the nose to the superior sagittal sinus. This has clinical importance in that infections of the nose and nearby areas can be transmitted to the meninges and brain from what is known as the danger triangle of the face.
TODO - check if this is what the FMA ID really denotes
Paired, endochondral bones formed by the fusion of the tibia and fibula. They form the shanks, extending from the knees to the ankles.
Paired, long bones of endochondral origin formed by the fusion of the radius and ulna.
The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)
The collection of all skeletal elements in an autopodium region.
Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]
The medial pterygoid (or internal pterygoid muscle), is a thick, quadrilateral muscle of mastication. The mandibular branch of the fifth cranial nerve, the trigeminal nerve, innervates the medial pterygoid muscle.
The medial pterygoid is a pharyngeal arch 1 muscle that participates in oral/pharyngeal behaviors and is innervated by the nerve to the medial pterygoid and attaches to the cranial base and the medial side of the mandibular angle.[FEED]
Pharyngeal arch 1 muscle that participates in oral/pharyngeal behaviors, is innervated by the lateral pterygoid nerve branches, and attaches to the condylar process of the mandible and temporomandibular joint (TMJ) capsule, and the cranial base.
Pharyngeal arch 1 muscle that participates in oral/pharyngeal behaviors, is innervated by the lateral pterygoid nerve branches, and attaches to the condylar process of the mandible and TMJ capsule, and the cranial base.[FEED]
either of the broad curved wing like expanses on each side of the sphenoid bone in adults; may exist independently in the young
The alisphenoid in mammals is part cartilage bone, part membrane bone[PMC1231738] In many mammals, e.g. the dog, the greater wing of the sphenoid bone stays through life a separate bone called the alisphenoid[WP].
The mammalian alisphenoid forms the greater wing of the sphenoid bone, which contributes a small part of the skull vault just caudal to the orbit, and also underlies the basal part of the frontal and parietal bones in the fetus (Iseki et al. 1997)
The handle of the malleus; the portion that extends downward, inward, and backward from the neck of the malleus; it is embedded throughout its length in the tympanic membrane.
Conical in shape, with the cone extending inwards (e.g. mammals) or outwards (e.g. in birds)
the central cone shaped core of spongy bone about which turns the spiral canal
The osseous spiral lamina is a bony shelf or ledge which projects from the modiolus into the interior of the canal, and, like the canal, takes two-and-three-quarter turns around the modiolus. It reaches about half-way toward the outer wall of the tube, and partially divides its cavity into two passages or scalae, of which the upper is named the scala vestibuli, while the lower is termed the scala tympani.
A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis.
this is not classified as a ligament in FMA
A corner of the outer (lateral) part of an eye.
The angle at the end of the palpebral fissure, the slit between the eyelids, close to the temporal region of the skull. [ISBN10:0124020607, p.263][VHOG]
segmentum laterale (lobus hepatis sinister)
segmentum mediale (lobus hepatis sinister)
the extravascular space in the liver between the parenchymal cells and a sinusoid that contains the blood plasma
A canthus is a corner of the eye where the upper and lower eyelids meet. The bicanthal plane is the transversal plane linking both canthi and defines the upper boundary of the midface.
paleodentate part of the dentate nucleus
Mammals typically have four parathyroids, while other groups typically have six
During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's].
The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview]
During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line.
The corneal limbus is the border of the cornea and the sclera (the white of the eye). The limbus is a common site for the occurrence of corneal epithelial neoplasm. Limbus contains radially oriented fibrovascular ridges known as the palisades of Vogt that may harbour a stem cell population[WP]. An annular transitional zone, approximately 1 mm wide, between the cornea and the bulbar conjunctiva and sclera. It is highly vascular and is involved in the metabolism of the cornea. It is ophthalmologically significant in that it appears on the outer surface of the eyeball as a slight furrow, marking the line between the clear cornea and the sclera. (Dictionary of Visual Science, 3d ed)[MeSH]
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
The zonule of Zinn (Zinn's membrane, ciliary zonule) is a ring of fibrous strands connecting the ciliary body with the crystalline lens of the eye. The zonule of Zinn is split into two layers: a thin layer, which lines the hyaloid fossa, and a thicker layer, which is a collection of zonular fibers. Together, the fibers are known as the suspensory ligament of the lens[WP]. Modified or toughened vitreous that suspend the lens at the equator to the non-pigmented epithelium of the ciliary zone. In zebrafish, dorsal zonules are thickened as compared to ventral zonules. In both dorsal and ventral regions, these fibers delimit the vitreous body aqueous humor boundary[ZFA].
Layer of nonkeratinized squamous epithelium lining the conjunctiva, overlying scleral tissue
In human anatomy, the anterior communicating artery is a blood vessel of the brain that connects the left and right anterior cerebral arteries. The anterior communicating artery connects the two anterior cerebral arteries across the commencement of the longitudinal fissure. Sometimes this vessel is wanting, the two arteries joining together to form a single trunk, which afterward divides; or it may be wholly, or partially, divided into two. Its length averages about 4 mm, but varies greatly. It gives off some of the anteromedial ganglionic vessels, but these are principally derived from the anterior cerebral artery. It is part of the cerebral arterial circle, also known as the circle of Willis.
The mouse has both left and right anterior vena cava. adult humans only have a right.
Trunk of systemic vein which is formed by the union of the right and left brachiocephalic veins and terminates in the right atrium[FMA:4720].
The hemispheric articular surface at the upper extremity of the thigh bone[Stedman, 26th ed]. The femur head is the highest part of the thigh bone. It is supported by the neck of the femur. The head is globular and forms rather more than a hemisphere, is directed upward, medialward, and a little forward, the greater part of its convexity being above and in front. Its surface is smooth, coated with cartilage in the fresh state, except over an ovoid depression, the fovea capitis femoris, which is situated a little below and behind the center of the head, and gives attachment to the ligament of head of femur. If there is a fracture of the neck of the femur, the blood supply through the ligament becomes crucial. In orthopedic surgery, the head of the femur is important because it can undergo avascular necrosis and consequent osteochondritis dissecans. The head is removed in total hip replacement surgery [WP].
Proximal head of the femur, which articulates with the acetabulum.[AAO]
germinal layer of the epiphyseal plate where cells are actively dividing as well as producing extracellular matrix[MP].
In this zone, chondrocytes undergo rapid mitosis, forming distinctive looking stacks[WP]
long bone epiphyseal plate proliferative zone
The layer of the epiphyseal plate of a long bone where chondrocytes mature and enlarge[MP].
there is also MA:0002849 ! hypertrophic cartilage zone
long bone epiphyseal plate hypertrophic zone
layer of the epiphyseal plate where new bone matrix is deposited[MP].
long bone epiphyseal plate ossification zone
secondary growth centers occurring as rings at the periphery of the superior and inferior surfaces of the vertebral body.
here epiphysis means deriving from a separate ossification center
embryologic structure that is formed by two longitudinal eminences, one on each alar plate of the midbrain. These eminences become the superior colliculus and inferior colliculus ( Carpenter-1983 )]
The term "tectal plate" (or "quadrigeminal plate") is used to describe the junction of the gray and white matter in the embryo. (NeuroNames ancil-453)
superficial white matter layer of superior collilculus that consists mainly of axions from the optic nerve.
superficial white layer of superior colliculus
A thin layer consisting of small myelinated axons together with marginal and horizontal cells.
we follow FMA is making this gray matter, but this needs to be reconciled with the WP-derived definition
The microstructure of the optic tectum / superior colliculus varies across species. As a general rule, there is always a clear distinction between superficial layers, which receive input primarily from the visual system and show primarily visual responses, and deeper layers, which receive many types of input and project to numerous motor-related brain areas. The distinction between these two zones is so clear and consistent that some anatomists have suggested that they should be considered separate brain structures. In mammals, neuroanatomists conventionally identify seven layers[WP].
cytoarchitectural part of superior colliculus
A central nervous system gray matter layer that is part of a superior colliculus.
gray matter layer of superior colliculus
A central nervous system white matter layer that is part of a superior colliculus.
predominantly white regional part of superior colliculus
white matter layer of superior colliculus
intermediate white layer of superior colliculus
stratum album intermediale of superior colliculus
stratum medullare intermedium colliculi superioris
intermediate white layer of the superior colliculus
superior colliculus intermediate white layer
middle white layer of superior colliculus
intermediate grey layer of superior colliculus
stratum griseum intermediale of superior colliculus
stratum griseum intermedium colliculi superioris
intermediate grey layer of the superior colliculus
middle gray layer of superior colliculus
stratum griseum profundum colliculi superioris
stratum griseum profundum of superior colliculus
deep gray layer of the superior colliculus
deep grey layer of the superior colliculus
superior colliculus intermediate deep gray layer
deep white matter layer of superior collilculus that consists entirely of fibers.
stratum album profundum of superior colliculus
deep white layer of the superior colliculus
superior colliculus intermediate deep white layer
The outermost layer of the superior colliculus.
grouping teleost assuming homology of superior colliculus and optic tectum[cjm]
superficial layer of superior colliculus
A layer of superior colliculus that lies between the superficial layer and the deep layer.
intermediate layer of superior colliculus
The innermost layer of the superior colliculus.
This grouping class is primarily to accommodate GO
visual processing part of nervous system
A region of the adult brain that processes the visual information from the compound eyes.
Large lobes of the brain associated with the eyes. In octopods and some squids the optic lobes may be separated from the rest of the brain by an optic stalk of varying length. In Octopus the optic lobes contain 92 million cells compared with only 42 million in the main central mass of the brain (J. Young, 1963) .
A group of neurons that provides a nervous signal to a tissue.
consider splitting epithelium from epithelial tissue
Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface.
Hemispherical structure on proximal epiphysis of humerus that articulates with glenoid cavity[WP,modified].
Hemispherical ball on the proximal end of the humerus that fits into the glenoid cavity of the pectoral girdle to form the shoulder joint[AAO].
A prominent unever rim that bounds the acetabulum, serving as the attachment for the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint.
The obturator foramen is the hole created by the ischium and pubis bones of the pelvis through which nerves and muscles pass.
Small opening for the passage of the obturatorius nerve that perforates the pubis.[AAO]
relationship loss: subclass pelvic girdle opening (AAO:0000767)[AAO]
Loose connective tissue which consists of an irregular network of cells and reticular fibers and is spatially associated with myeloid and lymphoid cells. Examples: stroma of bone marrow, stroma of spleen, stroma of lymph node.[FMA]
Network of reticular fibres (fine collagen) that form a soft skeleton to support the lymphoid organs (lymph nodes, bone marrow, and spleen).[AAO]
in FMA this is asserted as part of smooth muscle tissue
Medial end of the clavicle, which usually lies on the ventral side of the epicoracoid cartilage, just posterior to the epicoracoid bridge.
A bony projection on the distal epiphysis of the humerus that is the attachment site for the flexor muscles of the manus. This condyle faces posteriorly (for sprawling tetrapods) or medially (for erect tetrapods).
Rounded projection at the distal head of the humerus and medial to the humeral head, which serves as a place of attachment for the flexor muscles antogonistic to those that attach to the lateral epicondyle.[AAO]
A bony projection on the distal epiphysis of the humerus that is the attachment site for the extensor muscles of the distal parts of the forelimb. In humans, this is known as the lateral epicondyle, but the position varies across tetrapods.
Rounded projection at the distal head of the humerus (larger and more prominent than the lateral epicondyle) and lateral to the humeral head, which serves as a place of attachment for the mm extensor antebrachii et carpi radialis, extensor digitorum communis, and in part to the m extensor antebrachii et carpi ulnaris.[AAO]
Specialized connective tissue is a connective tissue, which consists of osteocytes and chondrocytes, the intercellular matrix of which is chondrified or calcified.[FMA]
made obsolete because FMA:37374 is a General anatomical term rather than a true class in the FMA
The olecranon is a large, thick, curved bony eminence of the forearm that projects behind the elbow. It is situated at the upper (proximal) end of the ulna, one of the two bones in the forearm. When the hand faces forward the olecranon faces towards the back (posteriorly). It is bent forward at the summit so as to present a prominent lip which is received into the olecranon fossa of the humerus in extension of the forearm. Its base is contracted where it joins the body and the narrowest part of the upper end of the ulna. Its posterior surface, directed backward, is triangular, smooth, subcutaneous, and covered by a bursa. Its superior surface is of quadrilateral form, marked behind by a rough impression for the insertion of the Triceps brachii; and in front, near the margin, by a slight transverse groove for the attachment of part of the posterior ligament of the elbow-joint. Its anterior surface is smooth, concave, and forms the upper part of the semilunar notch. Its borders present continuations of the groove on the margin of the superior surface; they serve for the attachment of ligaments, viz. , the back part of the ulnar collateral ligament medially, and the posterior ligament laterally. From the medial border a part of the Flexor carpi ulnaris arises; while to the lateral border the anconeus muscle is attached.
Large and thick process situated at the proximal (upper) end of the ulna. Its inner face forms the medial articular surface that articulates with the humeral head.[AAO]
The occipital condyles are undersurface facets of the occipital bone in vertebrates, which function in articulation with the superior facets of the atlas vertebra. The condyles are oval or reniform (kidney-shaped) in shape, and their anterior extremities, directed forward and medialward, are closer together than their posterior, and encroach on the basilar portion of the bone; the posterior extremities extend back to the level of the middle of the foramen magnum. The articular surfaces of the condyles are convex from before backward and from side to side, and look downward and lateralward. To their margins are attached the capsules of the atlantoC6ccipital articulations, and on the medial side of each is a rough impression or tubercle for the alar ligament. At the base of either condyle the bone is tunnelled by a short canal, the hypoglossal canal.
birds have a single occipital condyle, mammals have two[WP]
The mental foramen is one of two holes ('foramina') located on the anterior surface of the mandible. It permits passage of the mental nerve and vessels. The mental foramen descends slightly in edentulous individuals.
Structural framework that provides support to the nasal sacs and ducts.
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.[FMA]
Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]
The middle and longest portion of the sternum, lying between the manubrium superiorly and the xiphoid process inferiorly; it considerably lengthier, narrower, and thinner than the manubrium, attains its greatest breadth close to the lower end.
Proximal portion of the sternum, usually elaborated into a stylum that may be ossified.[AAO]
AAO defines as 'Proximal portion of the sternum, usually elaborated into a stylum that may be ossified' [AAO:0000939]
The head of ulna presents an articular surface, part of which, of an oval or semilunar form, is directed downward, and articulates with the upper surface of the triangular articular disk which separates it from the wrist-joint; the remaining portion, directed lateralward, is narrow, convex, and received into the ulnar notch of the radius.
The supporting bundles of muscular fibers lining the walls of the atria[MP].
Not present in any AO. Note that WP states that trabecular carnea are ventricular and 'They should not be confused with the pectinate muscles, which are present in the right and left atria only'
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003).
An anatomical space that surrounded_by a open tracheal system trachea.
An anatomical space that surrounded_by a trachea.
A subdivision of a the reproductive tract in a female organism that is the site of embryo development.
A tube that connects ovary to the uterus.
Endochondral tarsal bone that is medially located and between the intermedium and centralia.
One of two element that constitute the basal row of tarsals. The tibiale constitutes the postaxial element. In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the fibulare.[AAO]
The Tegmental Wall or Roof (paries tegmentalis) is formed by a thin plate of bone, the tegmen tympani, which separates the cranial and tympanic cavities. It is situated on the anterior surface of the petrous portion of the temporal bone close to its angle of junction with the squama temporalis; it is prolonged backward so as to roof in the tympanic antrum, and forward to cover in the semicanal for the Tensor tympani muscle. Its lateral edge corresponds with the remains of the petrosquamous suture[Grays] .
TODO - check AAO; grouping is made on basis of related synonym. Crista parotica: seems to be the same as the crista prootica. However, since this lateral ridge of the otic capsule is frequently formed by the opisthotic, rather than the prootic, this may be a better name.; Crista prootica: a ledge or ridge which elaborates the dorsal surface of the prootic or, more generally, the roof of the otic capsule, laterally. The crista may extend posteriorly & laterally, continuous with the paroccipital process, and/or anteriorly or anteroventrally to protect cranial nerve foramina and form part of the fenestra ovalis/vestibuli. In basal tetrapodomorphs and tetrapods, the crista prootica forms the floor of the posttemporal fenestra. See The Prootic. In many tetrapods, the crista prootica is not ossified, or incompletely ossified. However, in frogs, the crista is the main strut joining the skull roofing bones (frontoparietals) with the squamosals. The crista prootica has a similarly expanded role in mammals where it forms an important part of the epitympanic recess and anchors the tympanohyal.
Branch of spinal nerve that innervates the hypaxial muscles
Branch of spinal nerve that innervates the epaxial muscles
Groups of cells situated largely within the fiber bundles of the lateral lemniscus. Two nuclei are usually distinguished: a ventral group and a dorsal group (Brodal, Neurological Anatomy, 3rd ed., 1981, pg. 619).
not clear if the ZFA class denotes the same entity; check relationship to midbrain tegmentum - this leads to inconsistency with ABA. The FMA class should represnet the grouping, but there is no FMA class for the singular at the moment
Vein that is central to a lobule in the liver.
Microvessel of the lymphatic system lined with a single layer of overlapping endothelial cells. Joins to form the lymphatic vessels.
Microvessel of the lymphatic system lined with a single layer of overlapping endothelial cells.[TAO]
The initial segment of a cranial nerve, leaving the central nervous system.
recommend asserting under this class rather than relying on inference, as relations may change
A raised area of the biting surface of a tooth.
this class may be obsoleted and split - the TAO class is generic, the mammalian class refers specifically to a molariform tooth
Anatomical structure that is a natural outgrowth, prominence, or point that is part of the surface of a tooth.[TAO]
the elevated, somewhat pointed portions of the chewing surfaces on premolar and molar teeth
A muscle that moves a body part away from the sagittal plane/midline of the body[ZFA]. For example, the abductor muscles of the legs spread the legs away from the midline and away from one another. An abductor muscle opposes an adductor muscle[BTO].
A muscle that moves a body part away from the sagittal plane of the body.[TAO]
relationship loss: subclass cranial muscle (TAO:0001953)[TAO]
in FMA the Adbuctor muscle is a subclass of Relation. It's unclear what this actually means, we leave it here as a grouping for now
A nervous system commissure that connects a left hemisphere of cerebellum and connects a right hemisphere of cerebellum.
Diencephalic nucleus that is part of the superficial pretectum and is rostrally contiguous with the magnocellular superficial pretectal nucleus. Cells of the caudal pretectal nucleus are slightly smaller and less orderly around a central neuropil than those of the magnocellular superficial pretectal nucleus. From Neuroanatomy of the Zebrafish Brain.
Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage.
Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventrproperty_value external_definitionand forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583].
Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO]
relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO]
present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals.
chick scapula is of dual origin and segmentally organized
A peritubular capillary that is part of a cortex of kidney.
A region of nephron tubule that is part of a cortex of kidney.
cortical thick ascending limb of Henle's loop
kidney cortex loop of Henle ascending limb thick segment
renal cortex loop of Henle ascending limb thick segment
distal straight tubule postmacula segment
A muscular coat that is part of a ureter.
Structures in fishes homologous to the cortical tissue of the mammalian adrenal gland; they are in close proximity to or imbedded in the head kidney.
check isa - not a true gland? There are two types of interrenal cells identified (1) The noradrenaline type, which contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane. (2) The adrenaline type, in which the vesicles are smaller and contain homogenous electron-lucent granules that are separated from the vesicular membrane by a visible -- halo http://dev.biologists.org/content/130/10/2107.full
An epithelial structure consisting of steroid producing cells interposed with chromaffin cells embedded within the head kidney. The interrenal gland is thought to be the equivalent of the mammalian adrenal cortex in zebrafish. Hsu et al. 2003.[TAO]
consider ceding to TAO/ZFA - however, structure also present in cyclostomes
splanchnic mesoderm adjacent to urogenital ridge
This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
keep this grouping class so long as it is required for GO
Embryonic structure that forms from the anterior gut epithelium at the level of the second somite that then matures to form the swim bladder.
A thin membranous, sometimes alveolated sac in the dorsal portion of the abdominal cavity. Contains a varying mixture of gases, not identical to the composition of air. May be one, two or three chambered. May be connected to the gut by a tube, the ductus pneumaticus (then called physostomous) or unconnected (then called physoclistous). May function as one or more of:- hydrostatic organ, sound producing organ, sound receptor, respiratory organ. Found in Actinopterygii. Often lacking in bottom fishes.
Cavitated compound organ that is double-chambered, located in the coelom and used to maintain buoyancy and may function as an acoustic resonator.[TAO]
Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these.
The MA class is placed here because we assume it means diaphysis proper, because in MA epiphysis is not part of MA:0002803
A diaphysis that is part of a femur[Automatically generated definition].
The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur].
A proximal metaphysis that is part of a femur.
A distal metaphysis that is part of a femur.
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
The anal triangle is the posterior part of the perineum. It contains the anal canal. [WP,unvetted].
A specialized tract of tissue (as in the electric eel) in which electricity is generated.
TODO - request go term for function assignment; todo - add CL term for electrocyte
Organ that is used to produce an electric field, i.e. an electric organ discharge (EOD).[TAO]
modified muscle or nerve cells, which became specialized for producing bioelectric fields stronger than those that normal nerves or muscles produce (Albert and Crampton, 2006)
An endostyle is a longitudinal ciliated groove on the ventral wall of the pharynx which produces mucus to gather food particles. It is found in urochordates and cephalochordates, and in the larvae of lampreys. It aids in transporting food to the esophagus. It is also called the hypopharyngeal groove. The endostyle in larval lampreys (ammocetes) metamorphoses into the thyroid gland in adults, and is regarded as being homologous to the thyroid gland in vertebrates. However, Dumont, et al. question whether the endostyle in ammocetes is homologous with that of the urochordates and cephalochordates. Since the endostyle is found in the three branches of chordates, it is presumed to have arisen in the common ancestor of these taxa, along with a shift to internal feeding for extracting suspended food from the water.
Dumont, et al. question whether the endostyle in ammocetes is homologous with that of the urochordates and cephalochordates[WP].
the distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. hand, foot, paw)
EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER
An apical ectodermal ridge that is part of a handplate.
An autopod plate that has_potential_to_develop_into a manus.
the EHDAA2 term and the FMA term may not be exact equivalents - check
The part of the decidua in the pregnant human female lining the uterus.
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements UBERONREF:0000002 NC meeting scheme
Mesenchyme that is part of a mandibular prominence.
The lateral surface of the external nose ends below in a rounded eminence, the wing of the nose. It is elevated by the Levator labii superioris alaeque nasi muscle[WP]. the tissue comprising the lateral boundary of the nose, inferiorly, surrounding the naris[EoM].
The darker-colored muscle tissue of some mammals, composed of slow twitch muscle fibers.
check if relationship to cell types should be more specific type I cells
The fast and slow skeletal muscles are different in terms of twitching speed (Fitts 1994), and they are believed to be derived from distinct myogenic precursors (Stockdale 1992)
check if CALOHA term is for fiber or tissue. .
The paler-colored muscle tissue of some mammals, composed of fast twitch muscle fibers.
An anatomical space that surrounded_by a digestive tract.
A muscularis mucosa that is part of a urinary bladder.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]
A non-keratinized stratified squamous epithelium that is part of a tongue.
A parakeratinized epithelium that is part of a tongue.
A squamous epithelium that is part of a tongue.
this is a singleton subclass of tongue epithelium in MA
A squamous epithelium that is part of a esophagus.
MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass
A squamous epithelium that is part of a stomach.
The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane.
A squamous epithelium that is part of a vagina.
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.
A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
A mucosa of stomach that is part of a stomach glandular region.
stomach glandular region glandular mucous membrane
An epithelium that is part of a vestibular labyrinth.
inner ear vestibular component epithelium
Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue.
note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical
An epithelium that is part of a crista ampullaris.
epithelium of crista of ampulla of semicircular duct of membranous labyrinth
the epithelial cells lining the capsule and trabeculae of the thymus
TODO - check whether this is part of the thymus or borders it
the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals
The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis.
Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO]
There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis
A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra.
we use this as a generic grouping class for a number of taxa
in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct
An epithelium that is part of a efferent duct.
epithelium of efferent ductule of testis
The cervical loop is the location on an enamel organ in a developing tooth where the outer enamel epithelium and the inner enamel epithelium join. The cervical loop is a histologic term indicating a specific epithelial structure at the apical side of the tooth germ, consisting of loosely aggregated stellate reticulum in the center surrounded by stratum intermedium. These tissues are enveloped by a basal layer of epithelium known on the outside of the tooth as outer enamel epithelium and on the inside as inner enamel epithelium. During root formation the inner layers of epithelium disappear and only the basal layers are left creating Hertwig's Epithelial Root Sheath (HERS). At this point it is usually referred to as HERS instead of the cervical loop to indicate the structural difference[WP].
The stellate reticulum is a group of cells located in the center of the enamel organ of a developing tooth. These cells are star shaped and synthesize glycosaminoglycans. As glycosamingoglycans are produced, water is drawn in between the cells and stretch them apart. As they are moved further away from one another, the stellate reticulum maintain contact with one another through desmosomes, resulting in their unique appearance. stellate reticulum is lost after the first layer of dentin is laid down. this brings cells in inner enamel epithelium closer to blood vessels at the periphery[WP].
Inner layer of the dental organ, composed of ameloblasts[ZFA]. The inner enamel epithelium, also known as the internal enamel epithelium, is a layer of cells located on the rim nearest the odontogenic papilla of the enamel organ in a developing tooth. This layer is first seen during the bell stage. The location of the enamel organ where the outer and inner enamel epithelium join is called the cervical loop[WP].
Inner layer of the dental organ, composed of ameloblasts.[TAO]
Outer layer of the dental organ[ZFA]. a layer of cuboidal cells located on the periphery of the enamel organ in a developing tooth. This layer is first seen during the bell stage.
The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands.
The part of the mammary epithelium that consists of myo-epithelieal cells.
The inner lining of the cheeks and lips.
An epithelium that is part of a submandibular gland primordium.
submaxillary gland primordium epithelium
submandibular gland primordium epithelium
The Great Cardiac Vein (left coronary vein) begins at the apex of the heart and ascends along the anterior longitudinal sulcus to the base of the ventricles. It then curves to the left in the coronary sulcus, and reaching the back of the heart, opens into the left extremity of the coronary sinus. It receives tributaries from the left atrium and from both ventricles: one, the left marginal vein, is of considerable size, and ascends along the left margin of the heart.
A process which protrudes from the ventral caudal angle of the mandible, and acts as the attachment of the digastric muscle.
The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis.
The distal part of adenohypophysis: the part that makes up the main body of the gland.
Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO]
The anterior part of the adenohypophysis. [TFD][VHOG]
pars distalis of anterior lobe of pituitary gland
pars distalis lobi anterioris hypophyseos
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A capillary that is part of the coronary system.
A pointed projection of the skin on the head of various animals, consisting of a covering of horn (keratin and other proteins) surrounding a core of living bone.
An anatomical projection that is part of and protrudes from the head
revisit after CARO2 appendage issue is sorted. Note that antennae are appendages that protrude from the head
Antlers are the usually large, branching bony appendages on the heads of most deer species.
An exceretory tubule that usually opens to the exterior by a nephridiopore. The inner end of the tubule may be blind, ending in flame cells (protonephridium) or may open into the coelom through a ciliated funnel (metanephridium).
A network of dead-end tubules lacking internal openings found in the Phylums Platyhelminthes, kinorhyncha and Rotifera.
The ends are called flame cells (if cilliated) or solenocytes (if flagellated); they function in osmoregulation and ionoregulation. The terminal cells are located at the blind end of the protonephridium. Each cell has one or more cilia and their beating inside the protonephridial tube creates an outward going current and hence a partial pressurization in the blind of the tube. Because of this pressurization drives waste fluids from the inside of the animal, they are pulled through small perforations in the terminal cells and into the protonephridium. The perforations in the terminal cell are large enough for small molecules to pass, but larger proteins are retained within the animal. From the bottom of the protonephridium the solutes are led through the tube, formed by the canal cells, and exits the animal from a small opening formed by the nephridiopore. Selective reabsorption of useful molecules by the canal cells occurs as the solutes pass down the tubule. Protonephridia are generally found in basal organisms such as flatworms. Protonephridia likely first arose as a way to cope with a hypotonic environment by removing excess water from the organism (osmoregulation). Their use as excretory/ionoregulatory structures likely arose secondarily
A type of excretory gland or nephridium found in many types of invertebrates such as Annelids, Arthropods and Molluscs. It typically consists of a ciliated funnel opening into the body cavity or coelom connected to a duct which may be variously glandularized, folded or expanded (vesiculate) and which typically opens to the organism's exterior. These ciliated tubules pump water carrying surplus ions, metabolic waste, toxins from food, and useless hormones out of the organism through openings known as nephrostomes. This waste is passed out of the body at the nephridiopore. The primary urine produced by filtration of blood (or a similar functioning fluid) is modified into secondary urine through selective reabsorption by the cells lining the metanephridium. In many earthworms the nephridial ducts open into the digestive tract instead, a condition known as enteronephry.
Organs opening into the buccal cavity of pharynx (supposedly modified nephridia) of invertebrates.
Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface.
Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
A type of cell produced by division of the egg after fertilization.
A multicellular organism that is at the juvenile stage.
Whole organism that is not fully grown or sexually mature.[TAO]
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Whole organism that is fully grown or sexually mature.[TAO]
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
Portion of tissue that is posterior to the developing notochord during tail bud extension.
Portion of tissue is a posterior to the developing notochord during tailbud extension.[TAO]
Although there is mounting evidence showing the comparability of events and formation of different nascent tissue types during gastrulation and tail development, recent work also suggests the presence of an ongoing stem cell population capable of contributing to multiple tissue types in the tail of several different vertebrates, situated in the chordoneural hinge region of the tail bud. It would seem likely that secondary signaling centers regulate the fate to be adopted by such pluripotent progenitors.[well established][VHOG]
In mouse and chick, the derivative of the NSB (with a minor contribution from the CLE), the `chordo-neural-hinge'(CNH) (Cambray and Wilson, 2007; Catala et al., 1995; Charrier et al., 1999), contains progenitors for the ventral neural tube, somites and notochord (Cambray and Wilson, 2002; McGrew et al., 2008). The CNH is continuous with the most recently formed neural tube and notochord (Fig. 2C-D′). By contrast, the tissue immediately caudal to the CNH exclusively produces somites in mouse and chick (McGrew et al., 2008).
Cranial neural crest that migrates into the mandibular arch.
Cranial neural crest that migrates into the hyoid arch.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
A long narrow tube that joins the yolk-sac to the midgut lumen of the developing fetus.
In humans, it appears at the end of the fourth week, when the yolk-sac presents the appearance of a small pear-shaped vesicle (the umbilical vesicle). The vesicle can be seen in the afterbirth as a small, somewhat oval-shaped body whose diameter varies from 1 mm to 5 mm. It is situated between the amnion and the chorion and may lie on or at a varying distance from the placenta. Generally, the duct fully obliterates (narrows and disappears) during the seventh week, but a failure of the duct to close is termed a vitelline fistula. This results in discharge of meconium from the umbilicus. About two per cent of fetuses exhibit a type of vitelline fistula characterized by persistence of the proximal part of the vitelline duct as a diverticulum protruding from the small intestine, Meckel's diverticulum, which is situated about two feet above the ileocecal junction, and may be attached by a fibrous cord to the abdominal wall at the umbilicus. Sometimes a narrowing of the lumen of the ileum is seen opposite the site of attachment of the duct
One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively
The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.
An unctuous substance composed of sebum and desquamated epithelial cells, which covers the skin of the fetus.
A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
The rectouterine pouch (or rectouterine excavation, rectovaginal, Ehrhardt-Cole Recess or Pouch of Douglas) is the extension of the peritoneal cavity between the rectum and back wall of the uterus in the female human body. The rectouterine pouch is used in the treatment of end-stage renal failure in patients who are treated by peritoneal dialysis. The tip of the dialysis catheter is placed into the deepest point of the pouch. In women it is the deepest point of the peritoneal cavity, posterior to (behind) the uterus and anterior to (in front of) rectum. (The pouch on the other side of the uterus is the vesicouterine excavation. ) It is near the posterior fornix of the vagina. In men, the region corresponding to the rectouterine pouch is the rectovesical excavation, which lies between the urinary bladder and rectum. (There is no equivalent to the vesicouterine excavation.)
Poisonous animal secretions forming fluid mixtures of many different enzymes, toxins, and other substances. These substances are produced in specialized glands and secreted through specialized delivery systems (nematocysts, spines, fangs, etc.) for disabling prey or predator.
Note we include a separate class for snake venom
One of the first set of teeth in the growth development of humans and many other mammals[WP].
The set of teeth first in order or time of development that will be replaced by permanent dentition upon their loss.
The pit in the center of the abdominal wall marking the point where the umbilical cord entered in the fetus.
The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward.
The premolar teeth or bicuspids are transitional teeth located between the canine and molar teeth.
In humans, there are two premolars per quadrant, making eight premolars total in the mouth. They have at least two cusps. Premolars can be considered as a 'transitional tooth' during chewing, or mastication. It has properties of both the anterior canines and posterior molars, and so food can be transferred from the canines to the premolars and finally to the molars for grinding, instead of directly from the canines to the molars. The premolars in humans are the maxillary first premolar, maxillary second premolar, mandibular first premolar, and the mandibular second premolar. There is always one large buccal cusp, especially so in the mandibular first premolar. The lower second premolar almost always presents with two lingual cusps. Premolar teeth by definition are permanent teeth distal to the canines preceded by deciduous molars. In primitive mammals there are four premolars per quadrant. The most mesial two have been lost in Catarrhines. Paleontologists refer to human premolars as Pm3 and Pm4
A dermatome is an area of skin that is mainly supplied by a single spinal nerve. There are eight cervical nerves, twelve thoracic nerves, five lumbar nerves and five sacral nerves. Each of these nerves relays sensation (including pain) from a particular region of skin to the brain[WP].
A pharyngeal pouch that is between pharyngeal arches 1 and 2.
The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery
we use adjacency relations rather than part_of, as in EHDAA2.
A pharyngeal puch that is between the pharyngeal arches 2 and 3.
A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN10:0124020607][VHOG]
Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]
the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract.
Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve
A pharyngeal pouch that between pharyngeal arches 3 and 4.
A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN10:0124020607][VHOG]
Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]
The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve
A pharyngeal pouch between pharyngeal arch 4 and arch 5 or 6 (a fifth arch never establishes in amniotes).
A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN10:0124020607][VHOG]
Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]
Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands.
A pharyngeal pouch between pharyngeal arches 5 and 6.
Fifth of the pharyngeal (endodermal) evaginations between the visceral arches.[AAO]
pouches 5 and 6 are hard to distinguish. Rudimentary structure, becomes part of the fourth pouch contributing to thyroid C-cells
A pharyngeal pouch between pharyngeal arches 6 and 7.
Sixth of the pharyngeal (endodermal) evaginations between the visceral arches.[AAO]
in humans pouches 5 and 6 are hard to distinguish.
Along with the fourth pouch, contributes to the formation of the musculature and cartilage of the larynx
Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm.
The zebrafish head kidney consists of fused bilateral lobes located in the anterior part of the kidney. It is analogous to the mammalian bone marrow and the primary site of definitive hematopoiesis.
The zebrafish head kidney consists of fused bilateral lobes located in the anterior part of the kidney. It is analogous to the mammalian bone marrow and the primary site of definitive hematopoiesis. Davidson and Zon 2004.[TAO]
in GO, head kidney isa pronephros. Modified the ZFA relationships - the HK is derived from the anterior part of the pronephros and persists until adulthood
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
These folds of the rectouterine excavation are named the sacrogenital or rectouterine folds. They contain a considerable amount of fibrous tissue and non-striped muscular fibers which are attached to the front of the sacrum and constitute the uterosacral ligaments.
Mesothelium overs the body walls is called the parietal mesothelium
Mesothelium that covers the internal organs is called visceral mesothelium
An internal carotid artery that branching_part_of a left common carotid artery plus branches.
An internal carotid artery that branching_part_of a right common carotid artery plus branches.
A spinal artery that arises from the vertebral artery, adjacent to the medulla oblongata[WP,modified].
An anatomical cavity that surrounded_by a midgut.
An anatomical cavity that surrounded_by a hindgut.
One of the three branches of the thyroid axis that supplies the thyroid gland and branches to form the ascending cervical, esophageal, inferior laryngeal, muscular and tracheal arteries.
The superior thyroid artery arises from the external carotid artery just below the level of the greater cornu of the hyoid bone and ends in the thyroid gland.
Leaf of cardiac valve which has as its parts the anterior, and posterior leaflets that is attached to the chorda tendinea of left ventricle and to the frbrous ring of mitral valve.[FMA]
An intracranial venous sinus that lies in a midline location along the lower free border of the falx cerebri of the brain. The sinus receives blood from the great cerebral vein and joins the superior sagittal sinus posteriorly.
The blood vessel carrying deoxygenated blood that arises from the superior epigastric vein and empties into the external iliac vein.
In human anatomy, superior epigastric vein refers to a blood vessel that carries deoxygenated blood and drains into the internal thoracic vein. It anastomoses with the inferior epigastric vein at the level of the umbilicus and drains the anterior part of the abdominal wall and some of the diaphragm. Along its course, it is accompanied by a similarly named artery, the superior epigastric artery.
An anatomical cavity that surrounded_by a anal canal.
An anatomical cavity that surrounded_by a colon.
The medial arcuate ligament (also medial lumbocostal arch) is tendinous fascia that arches over the psoas major muscle as it passes through the diaphragm.
The lateral arcuate ligament (also lateral lumbocostal arch) is a ligament under the diaphragm that arches across the upper part of the quadratus lumborum. It is traversed by the subcostal nerve, artery and vein.
The superior meatus, the smallest of the three meatuses of the nose, occupies the middle third of the lateral wall of the nasal cavity. It lies between the superior nasal conchC& and middle nasal conchC&; the sphenopalatine foramen opens into it behind, and the posterior ethmoidal cells in front. The sphenoidal sinus opens into a recess, the sphenoethmoidal recess, which is placed above and behind the superior concha.
left dome of diaphragm viewed radiologically
right dome of diaphragm viewed radiologically
The long head originates on the supraglenoid tubercle just above the shoulder joint from where its tendon passes down along the intertubercular groove of the humerus into the joint capsule of the shoulder joint. [1] When the humerus is in motion, the tendon of the long head is held firmly in place in the intertubercular groove by the greater and lesser tubercles and the overlying transverse humeral ligament. During the motion from external to internal rotation, the tendon is forced medially against the lesser tubercle and superiorly against the transverse ligament.
Proximally (towards the body), the short head of the biceps attaches to (originates from) the coracoid process at the top of the scapula.
The squama of the occipital bone, situated above and behind the foramen magnum, is curved from above downward and from side to side.
See: http://purl.obolibrary.org/obo/uberon/tracker/58
The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border.
consider merging with UBERON:1500000 scapular blade, depending on https://github.com/obophenotype/uberon/issues/339. See also http://www.ncbi.nlm.nih.gov/pubmed/20136669
An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted]
An angle of the scapula formed by the junction of the superior and vertebral borders. It is thin, smooth, rounded, inclined somewhat lateralward, and gives attachment to a few fibers of the Levator scapulae[WP,unvetted]
A lamina propria that is part of a colonic mucosa.
lamina propria of colonic mucous membrane
A muscularis mucosa that is part of a colonic mucosa.
lamina muscularis of colonic mucous membrane
A serous membrane that is part of a uterine tube infundibulum.
serosa of infundibulum of fallopian tube
A muscle layer that is part of a uterine tube infundibulum.
muscle layer of infundibulum of fallopian tube
muscularis of infundibulum of uterine tube
muscle layer of infundibulum of uterine tube
A mesothelium that is part of a pericardio-peritoneal canal.
A visceral mesothelium that is part of a pericardium.
Found in all vertebrates, the VP (visceral pericardium) is also known as the cardiac epimysium. This outermost layer of the epicardium consists of a thin layer of mesothelial cells over a dense network of collagen and elastin fibers.[well established][VHOG]
mesothelium of visceral serous pericardium
A parietal mesothelium that is part of a pericardium.
EMAPA:16588 belongs here on the basis of exact synonym
mesothelium of parietal serous pericardium
A mesothelium that is part of a serous pericardium.
The inferior or orbital surface of the frontal lobe is concave, and rests on the orbital plate of the frontal bone. It is divided into four orbital gyri by a well-marked H-shaped orbital sulcus. These are named, from their position, the medial, anterior, lateral, and posterior orbital gyri. The medial orbital gyrus presents a well-marked antero-posterior sulcus, the olfactory sulcus, for the olfactory tract; the portion medial to this is named the straight gyrus, and is continuous with the superior frontal gyrus on the medial surface.
The vesicular gland is part of the male reproductive system. The vesicular gland contributes fluids, energy substrates, and buffers to semen. It can be found near the Coagulating gland, which also belongs to the reproductive system.
TODO - check this agaist seminal vesicle
bipartite seminal vesicles, with a seminal gland and vesicular gland sharing a common duct are found in lagomorphs
The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis.
The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
multicellular organism that can produce both male and female gametes.
An anatomical structure present only in hermaphrodites.
The vasculature consisting of brachiocephalic arteries and veins.
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
mesenchyme derived from head neural crest
Mesenchyme that develops_from a trunk neural crest.
mesenchyme derived from trunk neural crest
Paired thin medially aligned bar of cartilage that extends from the anterior end of the chondrocranium to just anterior to the anterior end of the notochord. The posterior ends of the trabeculae cranii are continuous with the parachordal cartilages, and they enclose the hypophyseal fenestra.
A paired cartilage element appearing in the preotic section of the head at the border between the brain and visceral structures (The Trabecula cranii: development and homology of an enigmatic vertebrate head structure - Cerny et al 2006)
Am embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
Of or pertaining to the period of time immediately following birth, or to the newborn.
The osseous cochlea is the bony foundation that forms the small shell arrangement for the cochlear nerve.
TODO - check this. in MA, cochlea is not part of the bony labyrinth
The entorhinal cortex (EC) is an important memory center in the brain. In rodents, the EC is located at the caudal end of the temporal lobe. In primates it is located at the rostral end of the temporal lobe and stretches dorsolaterally. It is usually divided into medial and lateral regions with three bands with distinct properties and connectivity running perpendicular across the whole area.
Connectivity notes: The medial entorhinal cortex preferentially connects with the postrhinal cortex, the presubiculum, visual association (occipital) and retrosplenial cortices[http://www.scholarpedia.org/article/Entorhinal_cortex]
Connectivity notes: The lateral entorhinal cortex, for example, is strongly connected to the perirhinal cortex, olfactory and insular cortex and the amygdala.[http://www.scholarpedia.org/article/Entorhinal_cortex]
The superior vestibular nucleus is the dorso-lateral part of the vestibular nucleus and receives collaterals and terminals from the ascending branches of the vestibular nerve. Its axons terminate in much the same manner as do those from the lateral nucleus.
vestibular nucleus of eighth cranial nerve
See comments for 'vestibular nuclear complex. Consider adding subclasses.
One of the nuclei comprising the vestibular nuclear complex. In some mammals, e.g., primates, it is further subdivided into subnuclei. It therefore differs in appearance and topology in different mammals.
relationship to Meckel's cartilage to be added
relationship to palatoquadrate to be added
A tunica media that is part of a artery.
A tunica adventitia that is part of a artery.
A tunica adventitia that is part of a vein.
The inferior olivary nucleus is the largest nucleus situated in the olivary body, part of the medulla oblongata.
Internal gray matter component which consists of an assemblage of nuclei of neuraxis. Example: cerebellar nuclear complex, Vestibular nuclear complex.[FMA]
TODO - move existing complex classes currently under nucleus to be under this class
Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.
this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.
The inferior olivary nucleus that is the smallest, and appears on transverse section as a curved lamina behind the primary olivary nucleus
inferior olivary complex, dorsal accessory olive
dorsal accessory inferior olivary nucleus
the lymph tissue on the floor of the oropharyngeal passage, near the root of the tongue
A nucleus of brain that is part of a preoptic area.
An intervertebral disk that is part of a cervical region of vertebral column. A cervical intervertebral disk connects at least one cervical vertebra, either to another cervical vertebra, or at one point on the vertebral colummn, to a thoracic vertebra
intervertebral disk of cervical vertebra
An intervertebral disk that is part of a thoracic region of vertebral column. A thoracic intervertebral disk connects at least one thoracic vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a lumbar vertebra
intervertebral disk of thoracic vertebra
An intervertebral disk that is part of a lumbar region of vertebral column. A lumbar intervertebral disk connects at least one lumbar vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra
An intervertebral disk that is part of a sacral region of vertebral column. A sacral intervertebral disk connects at least one sacral vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra
A intervertebral disk that connects a mammalian cervical vertebra 3 and connects a mammalian cervical vertebra 4.
intervertebral disk of third cervical vertebra
A intervertebral disk that connects a mammalian cervical vertebra 4 and connects a mammalian cervical vertebra 5.
intervertebral disc of fourth cervical vertebra
intervertebral disk of fourth cervical vertebra
A intervertebral disk that connects a mammalian cervical vertebra 5 and connects a mammalian cervical vertebra 6.
intervertebral disc of fifth cervical vertebra
intervertebral disk of fifth cervical vertebra
A intervertebral disk that connects a mammalian cervical vertebra 6 and connects a mammalian cervical vertebra 7.
intervertebral disk of sixth cervical vertebra
A intervertebral disk that connects a thoracic vertebra and connects a mammalian cervical vertebra 7.
intervertebral disk of seventh cervical vertebra
A intervertebral disk that connects a vertebral bone 2 and connects a mammalian cervical vertebra 3.
intervertebral disc of cervical vertebra 2
intervertebral disc of second cervical vertebra
intervertebral disk of cervical vertebra 2
intervertebral disk of second cervical vertebra
A intervertebral disk that connects a vertebral bone 1 and connects a vertebral bone 2.
intervertebral disc of cervical vertebra 1
intervertebral disc of first cervical vertebra
intervertebral disk of cervical vertebra 1
intervertebral disk of first cervical vertebra
A pre-cartilage condensation that is part of a trachea.
The upper esophageal sphincter (UES) (also called the Pharyngoesophageal sphincter) refers to the superior portion of the esophagus. Unlike the lower esophageal sphincter, it consists of striated muscle and is under conscious control. The primary muscle of the UES is the cricopharyngeus portion of the inferior pharyngeal constrictor. During swallowing the upper esophageal sphincter opens so the bolus can pass into the esophagus. A secondary role of the UES is to reduce backflow from the esophagus into the pharynx.
Any collection of muscles that is part of a pectoral appendage.
Any collection of muscles that is part of a pelvic appendage.
Musculature that is part of the pelvic fin.[TAO]
Any collection of muscles that is part of an appendage.
Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.
The collection of all skeletal elements in a pelvic appendage region.
A crista ampullaris neuroepithelium that is part of a anterior semicircular duct.
anterior semicircular canal sensory patch
anterior semicircular canal sensory patches
crista of ampulla of anterior semicircular duct of membranous laybrinth
A crista ampullaris neuroepithelium that is part of a posterior semicircular duct.
posterior semicircular canal sensory patch
posterior semicircular canal sensory patches
crista of ampulla of posterior semicircular duct of membranous laybrinth
A crista ampullaris neuroepithelium that is part of a lateral semicircular duct.
lateral semicircular canal sensory patch
lateral semicircular canal sensory patches
crista of ampulla of lateral semicircular duct of membranous laybrinth
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
Portion of tissue that is part of the heart tube and will become the sinus venosus.
A presumptive structure that has_potential_to_develop_into a atrioventricular canal.
Portion of tissue that is part of the heart tube and will become the atrioventricular canal.[TAO]
A presumptive structure that has_potential_to_develop_into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has_potential_to_develop_into a presomitic mesoderm.
A presumptive structure that has_potential_to_develop_into a primitive knot.
Presumptive structure fated to become the shield. Defined by fate mapping[ZFIN:curator].
A presumptive structure that has_potential_to_develop_into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
A presumptive structure that has_potential_to_develop_into a paraxial mesoderm.
A presumptive structure that has_potential_to_develop_into a floor plate.
A presumptive structure that has_potential_to_develop_into a bulbus arteriosus.
Portion of tissue that is part of the heart tube and will become the bulbus arteriosus.[TAO]
A presumptive structure that has_potential_to_develop_into a forebrain-midbrain boundary.
A presumptive structure that has_potential_to_develop_into a rhombomere 1.
A presumptive structure that has_potential_to_develop_into a rhombomere 3.
A presumptive structure that has_potential_to_develop_into a rhombomere 4.
A presumptive structure that has_potential_to_develop_into a rhombomere 5.
A presumptive structure that has_potential_to_develop_into a rhombomere 6.
A presumptive structure that has_potential_to_develop_into a rhombomere 7.
A presumptive structure that has_potential_to_develop_into a rhombomere 8.
A presumptive structure that has_potential_to_develop_into a rhombomere 2.
A presumptive structure that has_potential_to_develop_into a pronephric mesoderm.
A proximal convoluted tubule that is part of a pronephros.
A choroid plexus that is part of a cerebral aqueduct.
A blood vessel that is part of a pectoral appendage.
A blood vessel that is part of a limb/fin.
A vasculature that is part of a pectoral appendage.
A vasculature that is part of a chordate pharynx.
A vasculature that is part of a limb/fin.
A glomerular capillary that is part of a pronephros.
A glomerular basement membrane that is part of a pronephros.
A distal early tubule that is part of a pronephros.
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
Either the internal or external pudendal arteries.
The internal pudendal artery is an artery that branches off the internal iliac artery, providing blood to the external genitalia. The internal pudendal artery is the terminal branch of the anterior trunk of the internal iliac artery. It is smaller in the female than in the male.
The deep external pudendal artery (deep external pudic artery), more deeply seated than the superficial external pudendal artery, passes medialward across the Pectineus and the Adductor longus muscles; it is covered by the fascia lata, which it pierces at the medial side of the thigh, and is distributed, in the male, to the integument of the scrotum and perineum, in the female to the labium majus; its branches anastomose with the scrotal (or labial) branches of the perineal artery.
An artery that arises from the medial side of the femoral artery, close to the superficial epigastric artery and superficial iliac circumflex artery.
After piercing the femoral sheath and fascia cribrosa, it courses medialward, across the spermatic cord (or round ligament in the female), to be distributed to the integument on the lower part of the abdomen, the penis and scrotum in the male, and the labium majus in the female, anastomosing with branches of the internal pudendal artery. it crosses superficial to the inguinal ligament[WP]
Either of two main superficial veins of the leg, one larger than the other, that begin at the foot.
A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans.
In mice many lobules lack islets, in contrast to other mammals including humans
A duct that is part of the pancreas and connected to the duodenum.
this class groups together accessory (dorsal) and main (ventral) pancreatic ducts
Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms
thin keratinized layer of epidermis projecting from outer surface of beak[WP].
This covering arises from the Malpighian cells of the bird's epidermis,[9] growing from plates at the base of each mandible
A rhamphotheca that is part of a upper beak.
A rhamphotheca that is part of a lower beak.
The nidopallium, meaning nested pallium, is the region of the avian brain that is used mostly for some types of executive functions but also other higher cognitive tasks.
The region was renamed from neostriatum to nidopallium in 2002 during the Avian Brain Nomenclature Consortium because the prior name suggested that the region was used for more primitive functions
A pallial region found in avias that partially overlap regions homologous to the amygdala of mammals.
The arcopallium refers to regions of the avian brain which partially overlap regions homologous to the amygdala of mammals. These regions have formerly been referred to as archistriatum, and before this epistriatum or amygdaloid complex, and a recent change of nomenclature has divided the region into the arcopallium and posterior pallial amygdala. The new nomenclature, adopted in 2004, reflects a modern understanding that the avian brain is broadly similar to the mammalian brain, containing large regions homologous to the mammalian neocortex, claustrum, and pallial amygdala. The outdated nomenclature it replaced perceived the avian brain as consisting almost entirely of enlarged basal ganglia, to which more complex outer layers had been added during a progress toward mammalian intelligence. [Wikipedia:Arcopallium]
blood vessels supplying the stria vascularis in the cochlea of the inner ear.
A triangular plate of elastic fibrocartilage that forms the cartilage component of the pharyngotympanic tube.
cartilago tubae auditivae; cartilago tubae auditoriae
The bony part of pharyngotympanic tube is about 12 mm. in length. It begins in the carotid wall of the tympanic cavity, below the septum canalis musculotubarii, and, gradually narrowing, ends at the angle of junction of the squama and the petrous portion of the temporal bone, its extremity presenting a jagged margin which serves for the attachment of the cartilaginous portion.
A pouched enlargement of the gullet of many birds that serves as a receptacle for food and for its preliminary maceration.
we follow WP and place as part of the esophagus
Aves specific structure - consider adding functional grouping class. Kardong: some cetaceans have a crop-like structure
The glandular or true stomach of a bird that is situated between the crop and gizzard.
consider extending to crocodilians. EMAPA has proventricular region
The fourth stomach of ruminating animals. It is also called the 'true' stomach. It is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine. (From Black's Veterinary Dictionary, 17th ed)
Any of the first three stomachs of a ruminant, i.e., the rumen, reticulum, or omasum.
You will still see the statement in some texts that the parts of the forestomach are derived from the embryonic esophagus, and that's the reason why (like the esophagus) they're lined with stratified squamous epithelium. This is open to doubt. While there is no doubt that the rumen, reticulum, and omasum are all derived from the embryonic foregut, there is evidence to indicate that all three come from that an area of the foregut homologous to the part that develops into the single stomach of non-ruminants. If this is so, then the forestomach can be considered diverticula (or derivatives) of the stomach proper, not the esophagus, despite the nature of the lining -- http://www.vetmed.vt.edu/education/curriculum/vm8054/labs/lab21/Examples/exrumen.htm
The second stomach of ruminants. It lies almost in the midline in the front of the abdomen, in contact with the liver and diaphragm and communicates freely with the RUMEN via the ruminoreticular orifice. The lining of the reticulum is raised into folds forming a honeycomb pattern over the surface. (From Concise Veterinary Dictionary, 1988)
The third stomach of ruminants, situated on the right side of the abdomen at a higher level than the fourth stomach and between this latter and the second stomach, with both of which it communicates. From its inner surface project large numbers of leaves or folia, each of which possesses roughened surfaces. In the center of each folium is a band of muscle fibers which produces a rasping movement of the leaf when it contracts. One leaf rubs against those on either side of it, and large particles of food material are ground down between the rough surfaces, preparatory to further digestion in the succeeeding parts of the alimentary canal. (Black's Veterinary Dictionary, 17th ed)
The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity.
Coarse, partially chewed food is stored and churned in the rumen until the animal finds circumstances convenient for rumination. When this occurs, little balls of food are regurgitated through the esophagus into the mouth, and are subjected to a second more thorough mastication, swallowed, and passed on into other parts of the compound stomach. (From Black's Veterinary Dictionary, 17th ed)
There is no muscularis mucosae in the rumen. The rumen is lined by mucous membrane containing no digestive glands, but mucus-secreting glands are present in large numbers
The ruminants' stomach consists of four compartments: rumen, reticulum, omasum and abomasum. The first three compartments comprise the forestomach (proventriculus). They are lined with nonglandular membrane. The fourth compartment, the abomasum comprises the true stomach of the ruminants. It is lined with glandular mucous membrane. The rumen lies on the left of the abdominal cavity, the reticulum cranially and the omasum on the right. The abomasum lies ventrally, its proximal end lies ventral to the rumen, reticulum and omasum
Consider classifying each subdivision as 'stomach chamber'
An anatomical surface that is part of a tongue.
A incus endochondral element that is composed primarily of a cartilage tissue.
A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones.
check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO]
connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
The yellow spheroidal mass of stored food that forms the inner portion of the egg of a bird or reptile and is surrounded by the white.
Extraembryonic structure that serves as a nutrient store for the embryo during development.[AAO]
The majority of animals develop from a spherical egg with a single axis, the animal-vegetal (an-veg) axis. The animal half of the egg usually contains the nucleus of the oocyte, while the vegetal half of the egg is the preferred site for the storage of yolk. Eggs with an-veg polarity are considered ancestral for the vertebrates. Frogs, for example, have eggs with vegetally concentrated yolk and the nucleus located in the animal cytoplasm.[well established][VHOG]
The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food.
Dermal bone that is thin, flexible, and platelike, and that develops in overlapping skinfolds that cover the body and often the head of fish and the bases of the fins.
A fold in the surface epidermis composed of keratin[Kardong].
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
A lymphatic vessel that is part of a limb/fin.
A lymphatic vessel that is part of a pectoral appendage.
A lymphatic vessel that is part of a pelvic appendage.
A cartilage tissue that is part of a paired limb or fin.
Cartilage which is part of one of the paired fins.[TAO]
A cartilage tissue that is part of a pectoral appendage.
Cartilage which is part of the pectoral fin.[TAO]
A cartilage tissue that is part of a pelvic appendage.
Cartilage which is part of the pelvic fin.[TAO]
Midline nuclei found in the midbrain, includes the dorsal raphe nucleus and the rostral linear nucleus of raphe.
TODO - check. note BTO class is placed here as it is placed in hindbrain
set of raphe nuclei of tegmentum of midbrain
A nucleus of brain that is part of a pontine reticular formation.
A nucleus of brain that is part of a midbrain tegmentum.
this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
A nucleus of midbrain tegmentum that is part of a midbrain reticular formation.
any of the three large paired bundles of nerve fibers that connect the cerebellum to the brain stem
Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
A neural decussation that is part of a diencephalon.
The stratum intermedium in a developing tooth is a layer of two or three cells between the inner enamel epithelium and the newly forming cells of the stellate reticulum. It first appears during the early bell stage of tooth development, at around the 14th week of intrauterine life (in humans). The stratum intermedium has a notably high alkaline phosphatase activity. This layer, along with the inner enamel epithelium, is responsible for the tooth enamel formation. It is a part of the dental (enamel) organ.
A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.
Fluid anatomical entity containing cells.
Acellular anatomical structure whose predominant constituent is keratin.
should all structures composed primarily of keratin be classified here? At what stage of cornification are keratin-filled cells no longer considered cells
Acellular anatomical structure whose predominant constituent is chitin.
A domain of columnar epithelium in an embryo that represents the early stage of the development of the epithelial component of a new anatomical structure.
consider merging with ectodermal placode? In EHDAA2 this includes lens, nasal, otic epibranchial and trigeminal placodes
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
A collection of connected epithelial tubes with a single portal.
A complex of interlinking epithelial tubules.
A ring of smooth muscle cells whose contraction closes the opening of the ring.
A ring of striated muscle cells whose contraction closes the opening of the ring.
Mesenchyme with little extracellular matrix.
Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix.
this class will be an important part of the NC reorganization
obsoleted due to incorrect logical definition. A new class with the same name may be created in the future.
An anatomical structure that is undergoing regeneration.
we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure.
A portion of tissue that is regrowing after damage or amputation.[TAO]
An epithelium that extends its surface area by peripheral movement.
Part of the regeneration epithelium closest to the fin.[TAO]
A ciliated columnar epithelium that is part of a oviduct.
A cuboidal epithelium that is part of a oviduct.
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
Epithelium bearing vibratile cilia on the free surface.
Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP]
Stratified cuboidal epithelia is a rare type of epithelial tissue composed of cuboidally shaped cells arranged in multiple layers. They protect areas such as ducts of sweat glands, mammary glands, and salivary glands.
The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.
A muscle on the back of the forearm that extends the fingers and wrist.
Origin distal to extensor digitorum communis. The part of this muscle that gives a tendon to the 5th digit is comparable to the extensor digiti quinti proprius of the human [ISBN10:9780716717553]
The extensor minimi digiti (extensor digiti quinti proprius) is a slender muscle of the forearm, placed on the ulnar side of the Extensor digitorum communis, with which it is generally connected. It arises from the common Extensor tendon by a thin tendinous slip, from the intermuscular septa between it and the adjacent muscles. Its tendon runs through a compartment of the dorsal carpal ligament behind the distal radio-ulnar joint, then divides into two as it crosses the manus, and finally joins the expansion of the Extensor digitorum communis tendon on the dorsum of the first phalanx of the little finger[WP].
The tendon of insertion is sometimes divided and gives a slip to the fourth digit. An ulnar slip has been observed to end on the base of the fifth metacarpal, thus exactly reproducing the arrangement of the serially homologous slip known as peroneus tertius in the leg. The muscle may be absent in rare cases, but fusion with extensor digitorum is frequent, in which case the tendon comes from the common extensor.
Prostate gland lobe that in the mouse has the following characteristics: grossly, clear, gelatinous, and leaf-like; originates ventrally and wraps incompletely around the urethra dorsally, bilaterally. Simple columnar epithelium with the least amount of infolding. Secretory cells are oval and have slightly foamy cytoplasm; nuclei and basal nucleoli are inconspicuous. The secretion is pale and homogeneous. The stroma is thin
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
A synovial cavity of joint that is part of a hip joint.
MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together
A comb-like structure of blood vessels belonging to the choroid in the eye of a bird or reptile. It is non-sensory and is a pigmented structure that projects into the vitreous body from the point where the optic nerve enters the eyeball. The pecten is believed to both nourish the retina and control the pH of the vitreous body.
A wattle is a fleshy dewlap or caruncle hanging from various parts of the head or neck in several groups of birds, goats and other animals. In some birds the caruncle is erectile tissue.
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
the magnocellular nucleus projects to virtually all known major parts of the brain network that controls pelvic functions, including micturition, defecation, and penile erection, as well as to brain networks controlling nutrient and body water homeostasis. This and other evidence suggests that the magnocellular nucleus is part of a corticostriatopallidal differentiation modulating and coordinating pelvic functions with the maintenance of nutrient and body water homeostasis[PMID:16304682]
magnocellular nucleus of stria terminalis
The lateral septal area; largest nuclear mass in this region, plays a pivotal role in various physiological processes, such as aggression, emotion, thermoregulation, water and food intake and sexual behaviour.
Part of septal nuclear complex. In the human, it refers to the most caudal of scattered clusters of neurons in the septum pellucidum that extend, on the underside of the corpus callosum, from the level of the medial septal nucleus to the CA fields ( Crosby-1962 ). In the rat it is associated with the lateral septal nucleus throughout its rostro-caudal course toward the CA fields ( Swanson-1998. Adapted from Brain Info.
accessory olfactory bulb, glomerular layer
glomerular layer of the accessory olfactory bulb
accessory olfactory bulb glomerular layer
A nucleus embedded within the fibers of the trapezoid body.
A nucleus of the parabrachial area, which in the human brain is a horseshoe-shaped strip of gray matter comprising the Kölliker-Fuse nucleus, the lateral parabrachial nucleus and the medial parabrachial nucleus.
A neural nucleus that is part of a medulla oblongata.
A cytoarchitectural term denoting the layer of the CA3 field of the hippocampus that is deep to the Stratum pyramidale hippocampi and superficial to the Stratum radiatum (Hof-2000).
Regional part of fornix consisting of a thin layer of white matter on the surface of the hippocampal formation, bordering the wall of the lateral ventricle and composed of white, myelinated fibers. The alveus arises from cell bodies in the subiculum and hippocampus, and eventually merges with the fimbria of the hippocampus. The fimbria goes on to become the fornix (MM: 2006-10-26).
TODO - check xref: http://ncicb.nci.nih.gov/xml/owl/EVS/Alveus ! Alveus
A cytoarchitectural term denoting the outermost layer of the hippocampus (Stephan-75) (NeuroNames).
hippocampus stratum lacunosum moleculare
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP].
in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.
A small ligament attached to the superior surface of the pulmonary trunk and the inferior surface of the aortic arch. It is a nonfunctional vestige of the ductus arteriosus, and is formed within three weeks of birth. The ligamentum arteriosum is closely related to the left recurrent laryngeal nerve, a branch of the left vagus nerve. After splitting from the left vagus nerve, the left recurrent laryngeal loops around the aortic arch posterior to the ligamentum arteriosum, after which it ascends to the larynx[WP].
An inconstant lymph node of the anterior mediastinal group located adjacent to the ligamentum arteriosum.
A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes
A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx.
decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx
the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d
The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx.
The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer).
The junction between the esophagus and the stomach epithelium
squamocolumnar junction between esophagus and stomach
Anatomical structure in which parts of two or more anatomical structures establish physical continuity with one another or intermingle their component parts. Examples: gastroesophageal junction, line alba, knee joint.[FMA]
A sphincter that is part of an esophagus.
check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here
Developing nephron where the developing glomerular capsule has been invaded by a glomerular capillary loop called the glomerular tuft.
The lateral recess is a projection of the fourth ventricle which extends into the inferior cerebellar peduncle of the brainstem. The lateral aperture, an opening in each extremity of the lateral recess, provides a conduit for cerebrospinal fluid to flow from the brain's ventricular system into the subarachnoid space.
The anular ligament (orbicular ligament) is a strong band of fibers, which encircles the head of the radius (bone), and retains it in contact with the radial notch of the ulna
The vein that sprouts from the posterior cardinal vein, growing dorsally between the somites, and then joining, and draining the dorsal longitudinal anastomosing vessel.
Primary intersegmental vessels that are contacted by secondary angiogenic sprouts from the posterior cardinal vein and take on the characteristics of veins. These eventually link with other secondary sprouts from the posterior cardinal vein to form the parachordal vessel. Isogai et al. 2003.[TAO]
Cranial neural crest that is part of the facial region.
lateral mesenchyme derived from mesoderm
functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule.
consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts
region of the embryo into the area in which the kidney rudiment will develop.
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP].
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project.
A nucleus of brain that is part of a thalamus.
TODO - consider splitting nucleus and complex
The caroticotympanic branch (tympanic branch) is small; it enters the tympanic cavity through a minute foramen in the carotid canal, and anastomoses with the anterior tympanic branch of the internal maxillary, and with the stylomastoid artery.
An axon tract that is part of a spinal cord.
the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts
A tract that originates from neurons in the spinal central gray and projects to various somatosensory nuclei of the thalamus. It is formed in the medulla by merger of the anterior spinothalamic tract and lateral spinothalamic tract (adapted from Braininfo.org)
a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the spinal cord towards target cells in the thalamus. This axonal process is a member of those that make up the spinothalamic tract, one of the major routes of nociceptive signaling[GO][GO:0021963].
Regional part of superior cerebellar peduncle, located in the midbrain, consisting of a large bundle of fibers largely projecting from the deep cerebellar nuclei to the midbrain and thalamus. It is continuous with the superior cerebellar peduncle of the pons. (MM).
superior cerebellar peduncle of midbrain
pedunculus cerebellaris superior (mesencephalon)
superior cerebellar peduncle of the midbrain
FMA:72495 most likely denotes this class rather than the more generic parent, due to the part of relationship to pontine tegmentum.
pedunculus cerebellaris superior (pontis)
superior cerebellar peduncle of the pons
nucleus of the lateral lemniscus, horizontal part
intermediate nucleus of the lateral lemniscus
nucleus of the lateral lemniscus horizontal part
intermediate nucleus of lateral lemniscus
A bone that is part of a reproductive structure.
The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments.
The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes.
consider renaming: 'finger' is ambiguous as the term in some usages excludes the thumb (we include it)
An interphalangeal joint of manus that is part of a manual digit 1.
in humans, this connects proximal and distal phalanges of the thumb, so there is only a single inter-phalangeal joint - i.e. there is no distinct proximal and distal joints
interphalangeal joint of first digit of hand
An interphalangeal joint of pes that is part of a pedal digit 1.
interphalangeal joint of first digit of foot
interphalangeal joint of first digit of pes
An interphalangeal joint of pes that is part of a pedal digit 2.
interphalangeal joint of second digit of foot
An interphalangeal joint of pes that is part of a pedal digit 3.
interphalangeal joint of pedal digit III
interphalangeal joint of third digit of foot
An interphalangeal joint of pes that is part of a pedal digit 4.
interphalangeal joint of fourth digit of foot
An interphalangeal joint of pes that is part of a pedal digit 5.
interphalangeal joint of fifth digit of foot
An interphalangeal joint of manus that is part of a manual digit 2.
interphalangeal joint of manual digit II
interphalangeal joint of second digit of hand
An interphalangeal joint of manus that is part of a manual digit 3.
interphalangeal joint of manual digit III
interphalangeal joint of third digit of hand
An interphalangeal joint of manus that is part of a manual digit 4.
interphalangeal joint of fourth digit of hand
interphalangeal joint of manual digit IV
An interphalangeal joint of manus that is part of a manual digit 5.
interphalangeal joint of fifth digit of hand
A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 1.
metacarpophalangeal joint of first digit of hand
metacarpophalangeal joint of manual digit I
metacarpo-phalangeal joint of digit 1 of fore-paw
metacarpophalangeal joint of manual digit 1
A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 2.
metacarpophalangeal joint of manual digit II
metacarpophalangeal joint of second digit of hand
metacarpophalangeal joint of second finger
metacarpo-phalangeal joint of digit 2 of fore-paw
metacarpophalangeal joint of index finger
metacarpophalangeal joint of manual digit 2
A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 3.
metacarpophalangeal joint of manual digit III
metacarpophalangeal joint of third digit of hand
metacarpophalangeal joint of third finger
carpometacarpophalangeal joint of third digit
metacarpo-phalangeal joint of digit 3 of fore-paw
metacarpophalangeal joint of middle finger
metacarpophalangeal joint of manual digit 3
A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 4.
metacarpophalangeal joint of fourth digit of hand
metacarpophalangeal joint of fourth finger
metacarpophalangeal joint of manual digit IV
carpometacarpophalangeal joint of fourth digit
metacarpo-phalangeal joint of digit 4 of fore-paw
metacarpophalangeal joint of ring finger
metacarpophalangeal joint of manual digit 4
A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 5.
metacarpophalangeal joint of fifth digit of hand
metacarpophalangeal joint of fifth finger
metacarpophalangeal joint of manual digit V
metacarpo-phalangeal joint of digit 5 of fore-paw
metacarpophalangeal joint of little finger
metacarpophalangeal joint of manual digit 5
A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 1.
the name of the structure in EMAPA is incorrect
metatarsophalangeal joint of first digit of foot
metatarsophalangeal joint of pedal digit I
metatarsophalangeal joint of pedal digit 1
A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 2.
metatarsophalangeal joint of pedal digit II
metatarsophalangeal joint of second digit of foot
metatarsophalangeal joint of pedal digit 2
A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 3.
metatarsophalangeal joint of pedal digit III
metatarsophalangeal joint of third digit of foot
metatarsophalangeal joint of pedal digit 3
A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 4.
metatarsophalangeal joint of fourth digit of foot
metatarsophalangeal joint of pedal digit IV
metatarsophalangeal joint of pedal digit 4
A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 5.
metatarsophalangeal joint of fifth digit of foot
metatarsophalangeal joint of pedal digit V
metatarsophalangeal joint of pedal digit 5
ABA splits culmen into IV and V and IV-V
A medullary nucleus that sends its connections to the spinal cord in a mostly ipsilateral manner.
A medullary nucleus that sends its connections to the spinal cord in a mostly ipsilateral manner, although there is some decussation. It projects to the vermis in the anterior lobe, the pyramis and the uvula. The paramedian nucleus also projects to the contralateral PRN, the gigantocellular nucleus, and the nucleus ambiguous. The paramedian reticular formation is adjacent to the abducens (VI)nucleus in the pons and adjacent to the oculomotor nucleus(III) in the midbrain. The paramedian nucleus receives afferents mostly from the fastigial nucleus in the cerebellum and the cerebral cortex; however, the projections from the spinal cord are very sparse. The descending afferent connections come mostly from the frontal and parietal lobes; however the pontine reticular formation also sends projections to the paramedian reticular nucleus. There are also very sparse innervations from the superior colliculus. Lesions in the paramedian reticular nucleus have been shown to cause a stereotyped increase in the random patterns of motion in rats. The paramedian nuclei on either side of the brain stem have been shown to mediate the horizontal eye movements on their ipsilateral sides. It seems possible that that the random motion patterns of the above rats were caused by an inability to mediate their horizontal eye movements
The osphradium is the olfactory organ in certain molluscs, linked with the respiration organ. The main function of this is to test incoming water for silt and other possible food particles. It is used by all members of the Genus Conus.
A sweat that secreted_by a scrotal sweat gland.
A sweat gland that is part of a scrotum.
The teeth of adulthood that either replace or are added to the complement of deciduous teeth. (Boucher's Clinical Dental Terminology, 4th ed)
A tooth that forms after a primary tooth
A normal developing tooth which has not yet perforated the oral mucosa or one that fails to erupt in the normal sequence or time interval expected for the type of tooth in a given gender, age, or population group.
An endothelium that is part of a umbilical vein.
An endothelium that is part of a umbilical artery.
Body substance in liquid state, which is derived from plasma by passage through the (intact) wall of capillaries without further processing by secretory cells or glands.
Exudates are fluids, cells, or other cellular substances that are slowly discharged from blood vessels usually from inflamed tissues.
The serous fluid which accumulates in the peritoneal cavity in ascites.
TODO - move to pathological anatomical entity ontology
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
The complement of teeth in the jaws after the eruption of some of the permanent teeth but before all the deciduous teeth are absent. (Boucher's Clinical Dental Terminology, 4th ed)
A small, paired bony element (more rarely, having fused parts) located between the skull and the atlas in tuataras, crocodiles, chameleons, and many fossil reptiles; it is uncommon in turtles and mammals (hedgehog). The proatlas apparently develops from the ossified neural part of the sclerotome. Externally it resembles the neural arch of the vertebra, since it articulates anteriorly with the lateral occipital bone and posteriorly with the anterior articular process of the atlas.
Pygostyle refers to a number of the final few caudal vertebrae fused into a single ossification, supporting the tail feathers and musculature. In modern birds, the rectrices attach to these[WP].
A large gland at the base of a bird's tail dorsal to the cloaca at the end of the pygostyle that secretes an oil used in preening. It opens through a caudally directed nipple.
The gland is found near the base of the tail and is shaped into two symmetric parts. The oil of each part of the gland is secreted through the surface of the skin through a grease nipple-like nub. A bird will typically transfer this oil to its feathers by rubbing its head against the oil and then around the rest of the body. Tailward areas are usually preened utilizing the beak. Not all birds have a uropygial gland. Exceptions include the emu, ostrich, and bustards. These typically find other means to stay clean and dry, such as taking a dust bath
The uropygial gland is involved in maintaining feather condition and secretions spread by preening. It serves a waterproofing function. The secretions contain a pro-vitamin D, converted by UV light to active vitamin D. The secretions are also believed to suppress the growth of micro-organisms, serving an anti-bacterial function. [http://en.wikivet.net]
Sclerotic rings are rings of bone found in the eyes of several groups of vertebrate animals, except for mammals and crocodilians. They can be made up of single bones or small bones together. They are believed to have a role in supporting the eye, especially in animals whose eyes are not spherical, or which live underwater. Fossil sclerotic rings are known for a variety of extinct animals, including ichthyosaurs, pterosaurs, and dinosaurs, but are often not preserved[WP].
A region of the lower vertebral column formed from the fusion of vertebrae.
Complex of synostotically fused vertebrae supporting the pelvic girdle. In anurans, the synsacrum is formed by two vertebrae and the urostyle is fused to its posterior end.[AAO]
relationship loss: subclass portion of (AAO:0010428)[AAO]
In amphibians, a complex of synostotically fused vertebrae supporting the pelvic girdle. In anurans, the synsacrum is formed by two vertebrae and the urostyle is fused to its posterior end[AAO:Pugener_2002]
In birds and dinosaurs, the sacrum is extended by incorporation of additional fused or partially-fused caudal or lumbar vertebrae. The ilium of the pelvis is attached to the synsacrum and, in some species, may also be fused to it. Together with the pelvis this forms a rigid structure which carries the weight of the hind end of the animal. In living and some prehistoric birds, posterior to the synsacrum there are usually only a few free caudal vertebrae, on the end of which lies the pygostyle[Wikipedia:Synsacrum]
produced by fusion of last thoracics, all lumbars, all sacrals, & first few caudals;
A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord.
TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels
A vasculature that is part of a connecting stalk.
Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots.
The superficial layer (fascia of Camper) is a thick superficial layer of the anterior abdominal wall. It is areolar in texture, and contains in its meshes a varying quantity of adipose tissue. It is found superficial to Scarpa's fascia.
adipose layer of superficial fascia of abdomen
fatty layer of subcutaneous tissue of abdomen
fatty layer of superficial fascia of abdomen
intermediate investing fascia of abdomen
panniculus adiposus telae subcutaneae abdominis
superficial layer of superficial fascia of abdomen
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton.
Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]
Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]
present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species)
The greater alar cartilage (lower lateral cartilage) is a thin, flexible plate, situated immediately below the preceding, and bent upon itself in such a manner as to form the medial wall and lateral wall of the naris of its own side. The portion which forms the medial wall (crus mediale) is loosely connected with the corresponding portion of the opposite cartilage, the two forming, together with the thickened integument and subjacent tissue, the septum mobile nasi. The part which forms the lateral wall (crus laterale) is curved to correspond with the ala of the nose; it is oval and flattened, narrow behind, where it is connected with the frontal process of the maxilla by a tough fibrous membrane, in which are found three or four small cartilaginous plates, the lesser alar cartilages (cartilagines alares minores; sesamoid cartilages). Above, it is connected by fibrous tissue to the lateral cartilage and front part of the cartilage of the septum; below, it falls short of the margin of the naris, the ala being completed by fatty and fibrous tissue covered by skin. In front, the greater alar cartilages are separated by a notch which corresponds with the apex of the nose.
The part which forms the lateral wall is curved to correspond with the ala of the nose; it is oval and flattened, narrow behind, where it is connected with the frontal process of the maxilla by a tough fibrous membrane, in which are found three or four small cartilaginous plates, the lesser alar cartilages.
small cartilages of the nose connecting the greater alar cartilage and lateral nasal cartilage.
The lateral cartilage (upper lateral cartilage) is situated below the inferior margin of the nasal bone, and is flattened, and triangular in shape.[WP].
The vomeronasal cartilage (or Jacobson's cartilage) is a narrow strip of cartilage, low on the medial wall of the nasal cavity. It lies between the cartilaginous nasal septum and the vomer. The cartilage lies below, but is not connected to, the rudimentary vomeronasal organ of Jacobson[WP].
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
A reticular lamina of epithelium that is part of a spiral organ of cochlea.
reticular lamina of spiral organ of cochlea
A double layer composed of peritoneum that attaches the visceral organs to the body wall.
External part of the olfactory apparatus.
Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515].
A bone that is part of a appendage girdle region.
A bone that is part of a pectoral girdle region.
A bone element or fused bone that is part of pelvic girdle.
check sacrum, coccyx (MA does NOT include these)
typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone
A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.
Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]
Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]
The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts
the organ of balance composed of three long bony tubes of the labyrinth
consider adding FMA:60186 ! Semicircular canal here, as it is part of the bony labyrinth
A spinal cord ventral commissure that is part of a lumbar spinal cord.
A spinal cord ventral commissure that is part of a sacral spinal cord.
A spinal cord ventral commissure that is part of a cervical spinal cord.
cervical spinal cord anterior commissure
A spinal cord ventral commissure that is part of a thoracic spinal cord.
thoracic spinal cord anterior commissure
commissura alba posterior medullae spinalis
posterior white commissure of spinal cord
Dermal bone that develops from the fusion of the paired clavicle condensations in Archosauria. Serves as both an attachment site for pectoral musculature as well as a mechanical strengthening/ spacing element in the pectoral girdle. [PHENOSCAPE:ad].
currently assigned to be part of the pectoral girdle, but this may be incorrect if PG is a paired structure.
Found in both avian and non-avian theropods including, but not limited to: Coelophysoids, Allosauroids, Spinosauridae, Tyrannosauroids, Oviraptorosauria, Troodontidae and Dromaeosauridae
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
A posterior projection from proximal rib segments. Offers attachment sites for respiratory and shoulder muscles as well as adding structural support to the trunk skeleton[Kardong 2012].
Posteriorly directed process (occasionally directed anteriorly) usually associated with the rib (sometimes with the transverse process) of the third vertebra; they provide the origin of the mm serratus superior, medius, and inferior.[AAO]
WP: Although bony uncinate processes are unique to birds, cartilaginous uncinate processes are present in crocodiles. The uncinate process has also been reported in Sphenodon, Caudipteryx, oviraptorids, Confuciusornis and Chaoyangia however it does not occur in Archaeopteryx
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
Fibrous connective tissue that surrounds the notochord; includes a layer of elastin.
Portion of connective tissue which surrounds the notochord.[TAO]
relationship type change: part_of notochord (VSAO:0000032) CHANGED TO: surrounds notochord (UBERON:0002328)[VSAO]
Derived from cells surrounding the notochord (possibly the slerotome). Disparate from (not derived from) notochord.
A bone that is part of a craniocervical region.
A small bone occasionally found at the dorsal aspect of the wrist between the scaphoid, capitate, and trapezoid; it is developed as an independent cartilage in early foetal life but usually becomes fused with the scaphoid; it occurs normally in most monkeys.
TODO - check relationship to radial sesamoid
present in mouse[based on MA], carnivora[Websters] and macropods
A sesamoid bone that is part of a manus.
The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid.
A skeletal joint that is part of a appendage girdle region.
A anatomical surface that is part of a cartilage element.
FMA has multiple 'Articular surface of X' classes, with no way to group them
A tendon that attaches_to a biceps brachii.
A tendon that attaches_to a triceps brachii.
A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
subclasses of this should be checked for taxonomic consistency
Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
The tibiotarsus is the large bone between the femur and the tarsometatarsus in the leg of a bird. It is the fusion of the proximal part of the tarsus with the tibia. A similar structure also occurred in the Mesozoic Heterodontosauridae. These small ornithischian dinosaurs were unrelated to birds and the similarity of their pes bones is best explained by convergent evolution.
The tarsometatarsus is a bone that is found in the lower leg of certain tetrapods, namely birds. It is formed from the fusion of several bones found in other types of animals, and homologous to the mammalian tarsal (ankle) and metatarsal (pes) bones. Despite this, the tarsometatarsus of birds is often referred to as just the tarsus or metatarsus.
A muscle organ that is part of a pectoral girdle region.
EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate
The nail plate is the hard and translucent portion of the nail, composed of keratin.
Surface structure that is the anteriormost part of the lower jaw region.
Surface structure that is the anteriormost region of the lower jaw.[TAO]
In humans, the chin is the lowermost part of the face. It is formed by the lower front of the mandible. The chin developed as a point of muscular attachment facilitating minute movements of the lips associated with speech. In human evolution, the chin is a cladistic apomorphy, partially defining anatomically modern Humans as distinct from archaic forms
The part of the face above the eyes[MESH]. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond[WP].
A bony external plate or scale, as on the shell of a turtle, the skin of crocodilians, the feet of some birds. Scutes are similar to scales and serve the same function. Unlike the scales of fish and snakes, which are formed from the epidermis, scutes are formed in the lower vascular layer of the skin and the epidermal element is only the top surface. Forming in the living dermis, the scutes produce a horny outer layer, that is superficially similar to that of scales. Scutes will usually not overlap as snake scales (but see the pangolin). The outer keratin layer is shed piecemeal, and not in one continuous layer of skin as seen in snakes or lizards. The dermal base may contain bone and produce dermal armour. Scutes with a bony base are properly called osteoderms. Dermal scutes are also found in the feet of birds and tails of some mammals, and are believed to be the primitive form of dermal armour in reptiles. The term is also used to describe the heavy armour of the armadillo and the extinct glyptodon, and is occasionally used as an alternative to scales in describing snakes or certain fishes, such as sturgeons[WP].
Currently being reviewed by PHENOSCAPE:ad
we synonymize osteoderm and osteoscute with scute, see https://github.com/obophenotype/uberon/issues/516
in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone
The pelvic cavity is a body cavity that is bounded by the bones of the pelvis and which primarily contains reproductive organs, the urinary bladder, and the rectum. The pelvis is a marvel of physiology and is deceptively complex. It contains the lower urinary tract, reproductive system, lower digestive tract, major arteries and veins, muscle systems, nerve systems and bone systems. They all have to work together in a little crowded 'house'. It can be affected by many different diseases and by many drugs in many different ways. One part may impact upon another, for example constipation may overload the rectum and compress the urinary bladder, or childbirth might damage the pudendal nerves and later lead to anal weakness.
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
Either of two muscles of the calf of the leg.
Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax.
A muscle of back that is part of a lower back.
A muscle of back that is part of a dorsal thoracic segment of trunk.
A pennate muscle (also called a penniform muscle) is a muscle with fascicles that attach obliquely (in a slanting position) to its tendon. These types of muscles generally allow better stabilization and force production but less flexibility. Individual muscle fibers are formed into bundles of fasciculi and these bundles of fasciculi are formed into bundles of fascicles which compose the entire muscle itself. In a pennate muscle, the fascicles will form an angle with its central tendon. If all the fascicles are on the same side of the tendon, the pennate muscle is called unipennate. Examples of this include certain muscles in the manus. If there are fascicles on both sides of the central tendon, the pennate muscle is called bipennate. The rectus femoris, a large muscle in the quadriceps, is typical. If the central tendon branches within a pennate muscle, the muscle is called multipennate, as seen in the deltoid muscle in the shoulder.
the FMA class does not denote a muscle organ. editor note: TODO add child classes
The mouth of a starfish is located on the underside of the body, and opens through a short esophagus into firstly a cardiac stomach, and then, a second, pyloric stomach. Each arm also contains two pyloric caeca, long hollow tubes branching outwards from the pyloric stomach. Each pyloric caecum is lined by a series of digestive glands, which secrete digestive enzymes and absorb nutrients from the food. A short intestine runs from the upper surface of the pyloric stomach to open at an anus in the center of the upper body
One of the numerous external, fluid-filled muscular tubes of echinoderms, such as the starfish or sea urchin, serving as organs of locomotion, food handling, and respiration[BTO]. Tube feet consist of two parts: ampulla and podia. Ampulla contain both circular muscles and longitudinal muscle, whereas the podia contain the latter only. Thus the podia use suction to attach to the substratum[WP].
The pyloric ceca (or digestive glands) and the cardiac stomach produce digestive enzymes in starfishes. Digested material is absorbed through the pyloric ceca for transport to the rest of the body. Each pyloric cecum extends the length of each arm.
In starfishes the cardiac stomach is connected to a pyloric stomach which is located above it. Food can be brought into the stomach through the mouth or, in many species, the cardiac stomach can be extended out through the mouth to digest food outside the body. Suspension-feeding starfish use their tube feet to pass food to the mouth.
The water vascular system is a hydraulic system used by echinoderms, such as sea stars and sea urchins, for locomotion, food and waste transportation, and respiration.[1] The system is composed of canals connecting numerous tube feet. Echinoderms move by alternately contracting muscles that force water into the tube feet, causing them to extend and push against the ground, then relaxing to allow the feet to retract.[WP].
The constant contraction of ampulla (to extend and retract the tube feet) helps to move a starfish. The ampullae are teeth like structures surrounding the radial canal.
Within the mouth of a sea urchin is an elaborate five-sided jaw structure called Aristotles lantern that can be partially extruded from the mouth. It is able to grind up calcareous exoskeletons of plants and animals.
shaft of skeletal tissue that articulates with the lateral border of the carpus.
A clavicle that is in the right side of a entire appendicular skeleton.
A clavicle that is in the left side of a entire appendicular skeleton.
In the giant panda, a large digitlike preaxial element that articulates with the scapholunatum and the medial border of the first metacarpal.
A hard, thorny or needle-like structure which occurs on various animals. Animals such as porcupines and sea urchins grow spines as a self-defense mechanism. Spines are often formed of keratin. Other animals with spines are hedgehogs, spiny mice and at least two ornithischian dinosaurs.
May be reclassified depending on CARO treatment of appendage
A small wrench or claw-shaped structure commonly found on Echinoderms, particularly in sea stars (class Asteroidea) and sea urchins (class Echinoidea). Pedicellariae are poorly understood but in some taxa, they are thought to keep the body surface clear of algae, encrusting organisms, and other debris in conjunction with the ciliated epidermis present in all echinoderms. Pedicellariae in some taxa, such as the deep-sea Brisingida, and the Antarctic Labidiaster are known to function in food capture. In forcipulate sea stars, each pedicellaria is typically composed three forceps-like valves. Other asteroids can have pedicellariae composed of only two components. In some asteroid sea stars pedicellariae are present around the base of a spine or on the surface of the animal's body. In other sea stars, they are present in pits on the abactinal, marginal, or actinal surface; oftentimes on the adambulacral plate adjacent to the tube foot furrow.
Larval stage in echinoderms characterized by a planktonic and feeding larval form that possesses limb-like outgrowths bearing ciliated bands.
A planktonic and feeding larval form that possesses limb-like outgrowths bearing ciliated bands.
The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO].
The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html].
The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, http://en.wikipedia.org/wiki/Periodontal_fiber, http://purl.obolibrary.org/obo/uberon/tracker/21].
FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA
The left thoracic supracardinal vein loses its connection with the left posterior cardinal veins and left sinus horn and subsequently drains into the right supracardinal system.
The right supracardinal vein loses its connection with the posterior cardinal vein and makes a new anastomosis with the segments of the superior vena cava derived from the anterior cardinal vein, becoming the azygos vein.
An organic-inorganic composite material produced by some mollusks as an inner shell layer; it is also what makes up pearls. It is very strong, resilient, and iridescent. Nacre is found in some ancient lineages of bivalve gastropod and cephalopod. The inner layer in the great majority of mollusk shells is porcellaneous, not nacreous, frequently resulting in a non-iridescent shine or less commonly in non-nacreous iridescence such as flame structure (e.g. conch pearl). Pearls and the inside layer of pearl oyster and freshwater pearl mussel shells are made of nacre. Many other families of mollusk also have a nacreous inner shell layer, including marine gastropods such as the Haliotidae, the Trochidae and the Turbinidae. Nacre is composed of hexagonal platelets of aragonite (a form of calcium carbonate) 10-20 µm wide and 0.5 µm thick arranged in a continuous parallel lamina. These layers are separated by sheets of organic matrix composed of elastic biopolymers (such as chitin, lustrin and silk-like proteins)[WP].
A calcareous exoskeleton which encloses, supports and protects the soft parts of an animal in the phylum Mollusca, which includes snails, clams, tusk shells, and several other classes. Not all shelled molluscs live in the sea, many live on the land and in freshwater.
A highly complicated shield for the ventral and dorsal parts of the turtle, completely enclosing all the vital organs of the turtle and in some cases even the head. It is constructed of modified bony elements such as the ribs, parts of the pelvis and other bones found in most reptiles. The bone of the shell consists of both skeletal and dermal bone, showing that the complete enclosure of the shell probably evolved by including dermal armor into the rib cage.[WP].
Venoms from mollusks, including the Conus and Octopus species. The venoms contain proteins, enzymes, choline derivatives, slow-reacting substances, and several characterized polypeptide toxins that affect the nervous system. Mollusk venoms include cephalotoxin, venerup in, maculotoxin, surugatoxin, conotoxins, and murexine.
Dorsal subdivision of turtle shell, consisting of the animal's ribcage combined with dermal bone[WP, modified].
A composite bony plate forming the floor of the shell of a turtle consisting of fused dermal elements, including contributions from the clavicles (epiplastrons) and interclavice (epiplastron).
A giant secretory organelle that comprises a bulb-shape capsule containing a coiled hollow tubule structure attached to it. A cnida defines the phylum Cnidaria
Should be moved to GO. WP classifies as organelle but TOLweb says: A cnida therefore is technically not an organelle, but, rather, the most complex secretory product known
A cnida that is harpoon-like in structure and is capable of penetrating prey.
A cnida that is adhesive and lasso-like in structure and is capable of being projected at and wrapping around prey.
Venoms from jellyfish, corals, SEA ANEMONES, etc. They contain hemo-, cardio-, dermo- , and neurotoxic substances and probably ENZYMES. They include palytoxin, sarcophine, and anthopleurine.
A knoblike tooth primordium developing into an enamel organ surrounded by a dental sac and encasing the odontogenic papilla.
A central anatomical feature of a coiled snail shell or gastropod shell. It is often only clearly visible as a structure when the shell is broken, or sliced in half vertically, or in an X-ray.
The muscle of the central column or axis of a spiral univalve shell.
The rumen epithelium is the tissue which lines the largest of the four fore stomachs in the ruminant animal -cows and sheep. Rumen epithelial cells are important because they are responsible for the absorption of nutrients from the rumen into the blood.
The hollow basal portion of a feather below the vane[BTO]. At the base of the feather, the rachis expands to form the hollow tubular calamus (or quill) which inserts into a follicle in the skin. The basal part of the calamus is without vanes. This part is embedded within the skin follicle and has an opening at the base (proximal umbilicus) and a small opening on the side (distal umbilicus)[WP].
Collection of feather barbs that branch from rachis
A central shaft of feather, with two vanes either side.
A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus
A hairlike feather that grows alongside the down feathers.
In some passerines, filoplumes arise exposed beyond the contour feathers on the neck
One of a series of branches fused to the rachis (stem) of a feather. The barbs themselves also have branches called barbules, which have hooks that lock the barbs together[WP].
Pennaceous feathers are also known as contour feathers. This type of feather is present in most modern birds, and has been shown in some species of maniraptoran dinosaurs. Pennaceous feathers have a central shaft (or rachis) with vanes spreading to either side. These vanes are composed of a high number of flattened barbs, that are connected to one another with barbules. The barbules are tiny strands that criss-cross on the flattened side s of the barbs. This forms a kind of miniature velcro-like mesh that holds all the barbs together, stabilizing the vanes. Flight feathers (remiges and rectrices) are specialized types of pennaceous feathers, adapted for high loadings and often strongly asymmetric for improved flight performance[WP].
The perichondrium consists of two separate layers: an outer fibrous layer and inner chondrogenic layer. The chondrogenic layer remains undifferentiated and can form chondroblasts or chondrocytes.
inner chondrogenic layer of perichondrium
The perichondrium consists of two separate layers: an outer fibrous layer and inner chondrogenic layer. The fibrous layer contains fibroblasts, which produce collagenous fibers.
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
A short vessel of large caliber which arises from the internal pudendal between the two layers of fascia of the urogenital diaphragm; it passes medialward, pierces the inferior fascia of the urogenital diaphragm, and gives off branches which ramify in the bulb of the urethra and in the posterior part of the corpus spongiosum. It gives off a small branch to the bulbo-urethral gland.
The artery that serves blood to the penis. It subdivides into three arteries, the bulbourethral artery, the dorsal artery of the penis and the cavernosal artery.
TODO - split generic structure from arterial tree
The deep artery of the penis (artery to the corpus cavernosum), one of the terminal branches of the internal pudendal, arises from that vessel while it is situated between the two fascia of the urogenital diaphragm (deep perineal pouch). It pierces the inferior fascia, and, entering the crus penis obliquely, runs forward in the center of the corpus cavernosum penis, to which its branches are distributed.
The deep artery of clitoris is a branch of the internal pudendal artery.
with numerous vascular spaces that may become engorged with blood
Examples: corpus cavernosum or penis or clitoris
The space posterior to the glans clitoridis and between the labia minora, containing the openings of the vagina, urethra, and ducts of the greater vestibular glands.
A smooth muscle tissue that is part of a clitoris.
The white core of the inferior olivary nucleus of the medulla oblongata, most prominent medially.
A longitudinal sulcus on the anterior surface of the medulla oblongata, lateral to the pyramid, from which emerge the fibers of the hypoglossal nerve.
sulcus anterolateralis medullae oblongatae
anterolateral groove of medulla oblongata
sulcus ventrolateralis medullae spinalis
ventrolateral sulcus of medulla oblongata
The external junctural region between the lower part of the abdomen and the thigh.
In humans is the sole of the foot anatomically referred to as the plantar aspect. The equivalent surface in ungulates is the hoof
A saddle-shaped area that includes the nasal root and the lateral aspects of the nose. It lies between the glabella and the inferior boundary of the nasal bone, and extends laterally to the inner canth[WP].
The tissue that links the nasal tip to the nasal base, and separates the nares. It is the inferior margin of the nasal septum[EoM].
An epithelium that is part of a duodenum.
Epithelium pertaining to the trachea and bronchi.
The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions.
An epithelium that is part of a distal tubule.
An epithelium that is part of a buccal mucosa.
A mammary gland that is part of a inguinal part of abdomen.
A ridge of epidermal cells that will form the mammary placodes.
consider splitting ridge (precursor) and milk line
These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development
The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission.
A transverse foramen that is part of a vertebral bone 1.
A transverse foramen that is part of a vertebral bone 2.
main, posterior part of hyoglossus muscle (vs. chondroglossus) arising from the greater horn of the hyoid bone.
A vertebral foramen that is part of a cervical vertebra.
A vertebral foramen that is part of a lumbar vertebra.
A vertebral foramen that is part of a sacral vertebra.
A vertebral foramen that is part of a thoracic vertebra.
A neural arch that is part of a lumbar vertebra.
A neural arch that is part of a cervical vertebra.
A neural arch that is part of a sacral vertebra.
A neural arch that is part of a thoracic vertebra.
In a cervical vertebra, the posterior arch forms about two-fifths of the circumference of the ring: it ends behind in the posterior tubercle, which is the rudiment of a spinous process and gives origin to the Recti capitis posteriores minores.
A webbed interdigital region that is part of a manus.
webbed interdigital region between manual digits
A webbed interdigital region that is part of a pes.
webbed interdigital region between pedal digits
An autopod region that has_part a webbed interdigital region.
A manus that has_part a webbed interdigital region.
A pes that has_part a webbed interdigital region.
A digit that is part of a webbed autopod.
A muscle in the forearm and hand that flexes the thumb. It lies in the same plane as the flexor digitorum profundus. This muscle is unique to humans, being 'either rudimentary or absent' in other primates.
Modern humans are unique among hominids in having a flexor pollicis longus (FPL) muscle belly that is separate from that of the flexor digitorum profundus (FDP). While the FPL is not a separate muscle belly in extant great apes, a distinct tendon from the FDP belly might be present. In some individuals this tendon tend to act more like a ligament which restricts extension of the interphalangeal joint of the thumb. In orangutans there is a tendon similar in insertion and function to the FPL in humans, but which has an intrinsic origin on the oblique head of the adductor pollicis
Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation
The semilunar notch of the ulna (trochlear notch of ulna, greater sigmoid cavity) is a large depression, formed by the olecranon and the coronoid process, and serving for articulation with the trochlea of the humerus. About the middle of either side of this notch is an indentation, which contracts it somewhat, and indicates the junction of the olecranon and the coronoid process. The notch is concave from above downward, and divided into a medial and a lateral portion by a smooth ridge running from the summit of the olecranon to the tip of the coronoid process. The medial portion is the larger, and is slightly concave transversely; the lateral is convex above, slightly concave below.
A powerful flexor of the thigh at the hip joint (psoas major) and a weak flexor of the trunk and lumbar spinal column (psoas minor). Psoas is derived from the Greek 'psoa', the plural meaning 'muscles of the loin'. It is a common site of infection manifesting as abscess (PSOAS ABSCESS). The psoas muscles and their fibers are also used frequently in experiments in muscle physiology.
A muscle situated immediately behind the upper part of the Longus capitis that arises from the anterior surface of the lateral mass of the atlas, and from the root of its transverse process that inserts into the inferior surface of the basilar part of the occipital bone immediately in front of the foramen magnum.
A muscle that arises by a pointed tendon from the spinous process of the axis and inserts into the lateral part of the inferior nuchal line of the occipital bone and the surface of the bone immediately below the line.
extend and rotate the atlanto-occipital joint
A muscle that arise from the tubercle on the posterior arch of the and is inserted into the medial part of the inferior nuchal line of the occipital bone and the surface between it and the foramen magnum, and also takes some attachment to the spinal dura.
A prezygapophysis that is part of a lumbar vertebra.
cranial articular process of lumbar vertebra
superior articular process of lumbar vertebra
A prezygapophysis that is part of a sacral vertebra.
processus articularis superior (os sacrum)
processus articularis superior ossis sacri
superior articular process of sacral segment
superior articular process of sacral vertebra
A prezygapophysis that is part of a cervical vertebra.
superior articular process of cervical segment
superior articular process of cervical vertebra
A prezygapophysis that is part of a thoracic vertebra.
cranial articular process of thoracic vertebra
processus articularis (zygapophysis) thoracicus superior
superior articular process of thoracic vertebra
An postzygapophysis that is part of a lumbar vertebra.
caudal articular process of lumbar vertebra
inferior articular process of lumbar vertebra
An postzygapophysis that is part of a cervical vertebra.
inferior articular process of cervical vertebra
An postzygapophysis that is part of a thoracic vertebra.
caudal articular process of thoracic vertebra
inferior articular process of thoracic vertebra
processus articularis (zygapophysis) thoracicus inferior
The Abductor hallucis lies along the medial border of the pes and covers the origins of the plantar vessels and nerves. It arises from the medial process of the tuberosity of the calcaneus, from the laciniate ligament, from the plantar aponeurosis, and from the intermuscular septum between it and the Flexor digitorum brevis. The fibers end in a tendon, which is inserted, together with the medial tendon of the Flexor hallucis brevis, into the tibial side of the base of the first phalanx of the great toe.
The abductor pollicis brevis is a muscle in the manus that functions as an abductor of the thumb.
A thin layer of skeletal muscle that envelops the spermatic cord and testis of most male mammals in a series of loops; it is a continuation of the obliquus internus, arising from the inguinal ligament and inserting into the crest of the pubis and into the sheath of the rectus abdominis; it is innervated by the genital branch of the genitofemoral nerve and functions to draw the testis up toward the superficial inguinal ring in response to cold or to stimulation of the nerve;
in females it is represented by only a few muscle loops that envelop the round ligament of the uterus. This class represents the male structure
The smallest of the three gluteal muscles, situated immediately beneath the gluteus medius.
A muscle organ that is part of a olfactory apparatus.
The infrahyoid muscles are a group of four pairs of muscles in the anterior part of the neck. (The term infrahyoid refers to the region below to the hyoid bone in the neck. ) Collectively, they are referred to as the strap muscles, because the muscles are long and flat much like a strap.
The piriformis is a muscle in the gluteal region that originates from the anterior (front) part of the sacrum, the part of the spine in the gluteal region, and from the superior margin of the greater sciatic notch (as well as the sacroiliac joint capsule and the sacrotuberous ligament). It exits the pelvis through the greater sciatic foramen to insert on the greater trochanter of the femur. Its tendon often joins with the tendons of the superior gemellus, inferior gemellus, and obturator internus muscles prior to insertion[WP,modified].
The quadratus femoris is, as its name implies, a flat, quadrilateral skeletal muscle. Located on the posterior side of the hip joint, it is a strong lateral rotator and adductor of the thigh, but also acts to stabilize the femoral head in the Acetabulum.
The posterior fascial compartment of the thigh contains the knee flexors and hip extensors. It consists of the following muscles: biceps femoris semitendinosus semimembranosus The muscles here (except for the short head of the biceps femoris) are the hamstrings.
muscle of posterior compartment of thigh
A muscle that arises from the spinous processes of the third to the sixth thoracic vertebrae and inserts into the posterior tubercles of the transverse processes of the upper two or three cervical vertebrae[WP,modified].
Bilaterally: Extend the head & neck, Unilaterally: Lateral flexion to the same side, Rotation to the same side.
The iliocostalis cervicis (cervicalis ascendens) arises from the angles of the third, fourth, fifth, and sixth ribs, and is inserted into the posterior tubercles of the transverse processes of the fourth, fifth, and sixth cervical vertebrae..
One of the muscles deep to the prevertebral fascia on the anterior surface of the cervical and superior three thoracic vertebrae, symmetrically placed on each side of the median plane, including the longus colli, longus capitis, rectus capitis anterior, and rectus capitis lateralis muscles. innervated by anterior rami of cervical spinal nerves.
some authorities define the group as medial to the plane of the cervicobrachial plexus, and thus also include the anterior scalene muscle. Action notes: flexors of the head and neck
The term suprahyoid refers to the region above (superior to) the hyoid bone in the neck. The suprahyoid muscles include digastric, stylohyoid, geniohyoid, and mylohyoid.
The posterior cricoarytenoid muscles are extremely small, paired muscles that extend from the posterior cricoid cartilage to the arytenoid cartilages in the larynx. By rotating the arytenoid cartilages laterally, these muscles abduct the vocal cords and thereby open the rima glottidis. Their action opposes the lateral cricoarytenoid muscles. The posterior cricoarytenoid muscles receive innervation from the recurrent laryngeal branch of the vagus nerve (CN X). Paralysis of the posterior cricoarytenoid muscles may lead to asphyxiation as they are the only laryngeal muscles to open the true vocal folds, allowing inspiration and expiration.
The lateral cricoarytenoid (also anterior cricoarytenoid) muscles extend from the lateral cricoid cartilage to the ipsilateral arytenoid cartilage. By rotating the arytenoid cartilages medially, these muscles adduct the vocal cords and thereby close the rima glottidis, protecting the airway. (Their action is antagonistic to that of the posterior cricoarytenoid muscles. ) The lateral cricoarytenoid muscles receive innervation from the recurrent laryngeal branch of the vagus nerve (CN X).
The tranverse arytenoid crosses transversely between the two cartilages. It is an unpaired muscle running from one arytenoid to another to pull the arytenoids together.
The oblique arytenoid, the more superficial Arytenoid muscle, forms two fasciculi, which pass from the base of one cartilage to the apex of the opposite one, and therefore cross each other like the limbs of the letter X; a few fibers are continued around the lateral margin of the cartilage, and are prolonged into the aryepiglottic fold; they are sometimes described as a separate muscle, the Aryepiglotticus. The aryepiglottic muscle together with the transverse arytenoid and the thyroarytenoid work as a sphincter and close the larynx as we swallow or cough. Its innervation is by the recurrent laryngeal nerve (from vagus) just like all the intrinsic muscles of the larynx except the cricothyroid muscle.
The Thyroarytenoid is a broad, thin, muscle which lies parallel with and lateral to the vocal fold, and supports the wall of the ventricle and its appendix. It functions in fine tonal control of the vocal cords.
The vocal muscle is the upper portion of the thyroarytenoid muscle which is primarily involved in producing speech.
in FMA this is not placed under thyro-arytenoid but almost all sources consider this to be the case (confirmed with FEED:rd)
A muscle of the tongue that consists of a thin stratum of oblique and longitudinal fibers immediately underlying the mucous membrane on the dorsum of the tongue.
musculus longitudinalis superior linguae
A muscle of the tongue that consists of fibers which arise from the median fibrous septum and pass lateralward to be inserted into the submucous fibrous tissue at the sides of the tongue.
intrinsic tongue muscle transverse component
A muscle of the tongue that is found only at the borders of the forepart of the tongue. Its fibers extend from the upper to the under surface of the organ.
intrinsic tongue muscle vertical component
The levator veli palatini is the elevator muscle of the velum palatinum in the human body. During swallowing, it contracts, elevating the soft palate to help prevent food from entering the nasopharynx. It is innervated via the pharyngeal plexus, primarily by the vagus nerve (CN X). The levator veli palatini (Levator palati) is a thick, rounded muscle situated lateral to the choanC&. It arises from the under surface of the apex of the petrous part of the temporal bone and from the medial lamina of the cartilage of the auditory tube. After passing above the upper concave margin of the Constrictor pharyngis superior it spreads out in the palatine velum, its fibers extending obliquely downward and medially to the middle line, where they blend with those of the opposite side.
The levator veli palatini is part of the soft palate that attaches to the cranial base, pharyngotympanic tube and the soft palate and is innervated by Cranial Nerve X via the pharyngeal plexus.[FEED]
The tensor veli palatini (tensor palati) is a broad, thin, ribbon-like muscle in the head that tenses the soft palate.
The tensor veli palatini is a muscle of the soft palate that attaches to the cranial base and pharyngotympanic tube, wraps around the pterygoid hamulus and then attaches to the midline palatal raphe of the soft palate that is innervated by cranial nerve V3.[FEED]
The Procerus is a small pyramidal slip of muscle deep to the superior orbital nerve, artery and vein.
The depressor septi (Depressor alE nasi) arises from the incisive fossa of the maxilla. Its fibers ascend to be inserted into the nasal septum and back part of the alar part of nasalis muscle. It lies between the mucous membrane and muscular structure of the lip.
The Depressor Supercilii is an eye muscle of the human body. The nature of this muscle is in some dispute. Few printed anatomies include it (Netter, et al. ) and many authorities consider it to be part of the orbicularis oculi muscle . On the other hand, many dermatologists, ophthalmologists and plastic surgeons hold that the depressor supercilli is a distinct muscle and has a definite, individual effect on the movement of the eybrow and skin of the glabella.
The levator labii superioris alaeque nasi muscle is, translated from Latin, the 'lifter of the upper lip and of the wing of the nose'. It has the longest name of any muscle in an animal.
levator labii superioris alaequae nasi muscle
musculus levator labii superioris alaequae nasi
Facial muscle attached to the modiolus, corner (angle) of the mouth, and zygomatic bone. See Diogo 2008; Diogo et al., 2009; Burrows et al.., 2011., also DuBrul, 1980.
Facial muscle attached to the modiolus, corner (angle) of the mouth, and zygomatic bone. This muscle is ventral to the zygomaticus minor and dorsal to the platysma muscle. In many mammals this muscle also has an attachment to the cartilage of the external ear, in which case it is called the auriculolabialis inferior. See Diogo 2008; Diogo et al., 2009; Burrows et al.., 2011., also DuBrul, 1980.
musculus quadratus labii superioris, zygomatic head
square muscle of the upper lip, zygomatic head
The levator anguli oris (caninus) is a facial muscle of the mouth arising from the canine fossa, immediately below the infraorbital foramen. Its fibers are inserted into the angle of the mouth, intermingling with those of the Zygomaticus, Triangularis, and Orbicularis oris.
A muscle of facial expression, innervated by the facial nerve, attached to the skin of the lower lip and inferior to the lower lip (in humans this region is called the chin or mental region), the orbicularis oris muscle, and the mandible in the symphyseal region. See Diogo et al., 2009; Burrows et al., 2011)
The Depressor anguli oris (Triangularis) arises from the oblique line of the mandible, whence its fibers converge, to be inserted, by a narrow fasciculus, into the angle of the mouth.
Facial muscle that attaches to the fascia of the masseter muscle and the facia of the skin in the region of the corner (angle) of the mouth. Even in species in which this muscle is present, it is highly variable. A true risorius muscle may only be present in Hominins (humans and great apes). See Diogo 2008; Diogo et al., 2009; Burrows et al.., 2011., also DuBrul, 1980.
The Helicis major is a narrow vertical band situated upon the anterior margin of the helix. It arises below, from the spina helicis, and is inserted into the anterior border of the helix, just where it is about to curve backward.
The Helicis minor is an oblique fasciculus, covering the crus helicis.
The Tragicus is a short, flattened vertical band on the lateral surface of the tragus.
The Antitragicus arises from the outer part of the antitragus, and is inserted into the cauda helicis and antihelix.
The transverse muscle of auricle is placed on the cranial surface of the pinna. It consists of scattered fibers, partly tendinous and partly muscular, extending from the eminentia conchae to the prominence corresponding with the scapha.
The oblique muscle of auricle, on the cranial surface, consists of a few fibers extending from the upper and back part of the concha to the convexity immediately above it.
The transversus menti, or transverse muscle of the chin, is a facial muscle that is often considered to be the superficial fibers of the depressor anguli oris muscle which cross to the other side of the face.
Any of the three pairs of muscles in the lateral neck, namely the scalenus anterior, scalenus medius, and scalenus posterior. They are innervated by the spinal nerves C4-C8[WP].
A muscular partition formed by the levatores ani and coccygei, with which may be included the parietal pelvic fascia on their upper and lower aspects. It separates the pelvic cavity above from the perineal region below.
The Innermost intercostal muscle is a layer of intercostal muscle beneath the intercostal nerves and internal intercostal muscles. These are divided into transversus thoracis anteriorly, lateral muscle slips laterally and subcostalis posteriorly.
The Subcostales (Infracostales) consist of muscular and aponeurotic fasciculi, which are usually well-developed only in the lower part of the thorax; each originates from the inner surface of one rib, and is inserted into the inner surface of the second or third rib above, near its angle. Their fibers run in the same direction as those of the Intercostales interni.
The Scalenus anterior (Scalenus anticus), also known as anterior scalene muscle, lies deeply at the side of the neck, behind the Sternocleidomastoideus. It arises from the anterior tubercles of the transverse processes of the third, fourth, fifth, and sixth cervical vertebrC&, and descending, almost vertically, is inserted by a narrow, flat tendon into the scalene tubercle on the inner border of the first rib, and into the ridge on the upper surface of the rib in front of the subclavian groove.
The stylohyoid muscle is a slender muscle, lying anterior, and superior of the posterior belly of the digastric muscle. It shares this muscle's innervation by the facial nerve.
The stylohyoid is a pharyngeal arch II muscle that participates in oral/pharygeal behaviors and is innervated by the stylohoid branch of the facial nerve and attaches to the stylohyal.[FEED]
pectoral girdle and thoracic body wall skeletal muscle
A muscle tissue that is part of a prostate gland.
An opening on medial margin of the kidney leading into the renal sinus. he renal vessels enter/leave the kidney at the hilum; the renal pelvis leaves the kidney at the hilum.
A proximal epiphysis that is part of a tibia.
A proximal epiphysis that is part of a fibula.
The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula].
A thin monolayer of small cuboidal cells that make up the lower layer of the bilaminar embryonic disc, beneath the epiblast.
This layer can be distinguished from the overlying epiblast in the mouse embryo as early as day 4.5, and day 7 in human). The cells of the hypoblast are not thought to contribute to the developing embryo proper, but contribute to several extraembryonic structures. In rodents, the hypoblast cells form the parietal endoderm, parietal and visceral yolk sac as well as extraembryonic membranes, such as the extraembryonic endoderm, the yolk sac and the stalk that links it to the endodermal digestive tube. In human embryos, hypoblast cells migrate and line the blastocoelic cavity of the blastocyst, forming the primary yolk sac and Heuser's membrane. Although both the murine parietal yolk sac and the human primary yolk sac are transient structures, they are not developmental equivalents. A second wave of hypoblast cells migrates to form the definitive yolk sac which displaces the primary yolk sac and is equivalent to the murine visceral yolk sac. The primary yolk sac breaks up into small vesicles that can persist at the mural (abembryonic) pole.
Musculature that is derived from the hypaxial myotome region, trunk muscles that lie ventral to the horizontal septum of the vertebrae. Hypaxial muscles include some vertebral muscles, the diaphragm, the abdominal muscles, and all limb muscles.
Trunk muscle that lies ventral to the horizontal septum of the vertebrae.[AAO]
The hypaxial muscles are located on the lower side of the body, often below the horizontal septum in many species (primarily fish and amphibians). In amniotes, the positional distinctions have been lost as the body's muscles have changed through evolution, but in all species, the hypaxial muscles are innervated by the ventral ramus of the spinal nerves, while the epaxial muscles are innervated by the dorsal ramus.
Musculature that is derived from the epaxial myotome region, ventral to the horizontal septum of the vertebrae. Epaxial muscles include other (dorsal) muscles associated with the vertebrae, ribs, and base of the skull.
Trunk muscles that lies dorsal to the horizontal septum.[AAO]
the muscles derived from the medial myotome; includes the intrinsic back muscles
In humans, the erector spinae, the transversospinal muscles (including the multifidus, semispinalis and rotatores), the splenius and suboccipital muscles are the only epaxial muscles
The Subclavius is a small triangular muscle, placed between the clavicle and the first rib. Along with the pectoralis major and pectoralis minor muscles, the subclavius muscle makes up the anterior wall of the axilla.
An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers
The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5.
An epiblast (generic) that develops_from a blastodisc.
The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation. Kimmel et al, 1995.[TAO]
relationship type change: subclass embryonic structure (VSAO:0000178) CHANGED TO: develops_from embryonic structure (UBERON:0002050)[TAO]
relationship type change: subclass embryonic structure (VSAO:0000178) CHANGED TO: part_of embryonic structure (UBERON:0002050)[TAO]
part of blastodisc in BTO; indirect development in ZFA: df DEL df deep blastomere isa blastomere po blastodisc
The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein.
A limb segment that is part of a hindlimb.
A limb segment that is part of a forelimb.
A knob-like feature on the medial side of the femur that serves as a muscle attachment.
The fourth trochanter first appeared in the Erythrosuchidae, large basal archosaurian predators of the early Triassic period. This seemingly insignificant detail may have made the evolution of dinosaurs possible (all early dinosaurs and many later ones were bipeds), and may also be connected with the ability of the archosaurs or their immediate ancestors to survive the catastrophic Permian-Triassic extinction event[WP].
The infratentorial compartment that contains the CEREBELLUM and BRAIN STEM. It is formed by the posterior third of the superior surface of the body of the sphenoid (SPHENOID BONE), by the occipital, the petrous, and mastoid portions of the TEMPORAL BONE, and the posterior inferior angle of the PARIETAL BONE.
Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity
todo - review the relationships for this and its subclasses; the relation should be bounded rather than part of, and contains should be used for the brain parts contained by the fossae
A ridge or fold, such as the rugae of the stomach, which are large folds in the mucous membrane of that organ.
As currently defined this encompasses only mucuous membranes, and not for example rugal folds of skin such as the scrotal rugae
A masticatory vestige on the hard palate; one of several irregular, sometimes branching, crests of soft tissue that radiate from the region of the incisive papillae at their most anterior parts and extend a slight distance backward, crossing the hard palate and reaching laterally for variable distances.
this class refers to the singular and the FMA class refers to the set. In future this class may be split.
primitive endoderm-derived tissue that lines the luminal surface of the mural trophectoderm[MP]
A pocketlike fold of skin in the cheeks of various animals, such as squirrels, gophers, and monkeys, that functions as a means of carrying food.
The stylopharyngeus is a muscle in the head that stretches between the styloid process and the pharynx.
The stylopharyngeus is a pharyngeal arch III muscle that participates in oral/pharyngeal behaviors and is innervated by the n. to stylopharyngeus branch of the glossopharyngeal n. and attaches to the hyoid apparatus and the pharynx.[FEED]
The gingival sulcus is an area of potential space between a tooth and the surrounding gingival tissue and is lined by sulcular epithelium. The depth of the sulcus (Latin for groove) is bounded by two entities: apically by the gingival fibers of the connective tissue attachment and coronally by the free gingival margin.
The anterior lobe of the prostate gland.
the rodent prostate lobe that lies in the triangular area between urethra and seminal vesicle
In the maxilla, occasionally two additional canals are present in the middle line of the palatine process; they are termed the foramina of Scarpa, and when present transmit the nasopalatine nerves, the left passing through the anterior, and the right through the posterior canal.
One branch of the posterior superior nasal branches (trigeminal, maxillary branch), longer and larger than the others, is named the nasopalatine nerve (sometimes called the long sphenopalatine nerve). It enters the nasal cavity through the sphenopalatine foramen, passes across the roof of the nasal cavity below the orifice of the sphenoidal sinus to reach the septum, and then runs obliquely downward and forward between the periosteum and mucous membrane of the lower part of the septum. It descends to the roof of the mouth through the incisive canal and communicates with the corresponding nerve of the opposite side and with the greater palatine nerve. It supplies the palatal structures around the upper central and lateral incisors and the canines (the upper front six teeth). It also furnishes a few filaments to the mucous membrane of the nasal septum. The medial superior posterior nasal branches of maxillary nerve usually branches from the nasopalatine nerve.
An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP].
this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition
Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]
one of a pair of intromittent organs of male squamates. Hemipenes are usually held inverted, within the body, and are everted for reproduction via erectile tissue like that in the human penis. Only one is used at a time, and some evidence indicates males alternate use between copulations. The hemipenis itself has a variety of shapes, depending on species. Often the hemipenis bears spines or hooks, in order to anchor the male within the female. Some species even have forked hemipenes (each hemipenis has two tips). Due to being everted and inverted, hemipenes do not have a completely enclosed channel for the conduction of sperm, but rather a seminal groove which seals as the erectile tissue expands
The part of the cochlear labyrinth where the scala tympani and the scala vestibuli meet. It is the main component of the cochlear apex. The hair cells in this area best detect low frequency sounds.
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
An organ formed from the perforation between the point of contact between ectoderm and endoderm in the pharynx. The slits assist in filtering food particles from the water.
requires review. Kardong uses the term pharyngeal slit for Chondrichthyans. 'branchial slit' may also be used for amniote structures.
An endoderm that is part of a thymus primordium.
The superior mediastinum is that portion of the interpleural space which lies between the manubrium sterni in front, and the upper thoracic vertebrae behind.
Anterior, middle and posterior mediastinum.
The anterior mediastinum exists only on the left side where the left pleura diverges from the mid-sternal line. It is narrow, above, but widens out a little below.
The middle mediastinum is the broadest part of the interpleural space. It is made up of the pericardial sac and its contents.
The posterior mediastinum is an irregular triangular space running parallel with the vertebral column.
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
Any duct branching of of the main epididymis duct.
Secretion produced by Type 2 pulmonary alveolar cell.
the dilated area of tissue where the stomach and esophagus meet
Non-glandular portion of the stomach of some mammals that is connected to the esophagus. It is utilized as a holding chamber during digestion for un-digested and partially digested food.
The mouse stomach contains two well-defined areas, a (nonglandular) forestomach and a glandular stomach, which are separated by the limiting ridge (margo plicatus)[http://ctrgenpath.net/static/atlas/mousehistology/Windows/digestive/forestomach.html].
This class is based on the murine structure. Other groups, such as cetaceans, also have a forestomach (which is essentially an enlargement of the esophagus)
The anterior part of the body of the sphenoid bone in front of the basisphenoid. It is usually a separate bone in the young or fetus, but becomes a part of the sphenoid in the adult.
transient layer of the cerebellar cortex present during development which is composed of dividing and migrating granule cells[MP]
The transient layer of the cerebellar cortex present during development which is composed of the dividing and migrating granule cell[MGI:tc]
The granule neurons migrate from the exterior layer to form an inner layer known as the internal granule layer. The external granular layer ceases to exist in the mature cerebellum, leaving only granule cells in the internal granule layer[WP]
outer granular layer of cerebellar cortex
inner granular layer of cerebellar cortex
A concavity in the floor of the cochlear duct formed by the overhanging vestibular lip.
A concavity in the outer wall of the cochlear duct between the spiral prominence and the spiral organ.
The great auricular nerve originates from the cervical plexus, composed of branches of spinal nerves C2 and C3. It provides sensory innervation for the skin over parotid gland and mastoid process, and both surfaces of the outer ear.
TODO - check MA grouping; in MA this is part_of pinna - should this be a different relationship?
The first body segment in annelids worms. It is in front of (but does not include) the mouth, being usually a small shelf- or lip-like extension over the dorsal side of the mouth. It sometimes bears antennae and eyes. By feeding, it often functions like a kind of overlip. The shape and composition of prostomium are important for annelid systematics.
It sometimes bears antennae and eyes. It often functions like a kind of overlip when the animal is feeding. The shape and composition of prostomium are important for annelid systematics.
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10
The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
A thick, spongy layer of tissue located under the metacarpal and metatarsal joints of the autopod
An autopod pad that is in the metacarpal region
An autopod pad that is in the metatarsal region
The canine metatarsal pad is large and heart-shaped, and functions to cushion the foot. The pad is covered by a naked, densely cornified epidermis, which is usually highly pigmented and is the toughest region of the canine skin. The digital cushion or bulk of the foot pad is composed of a subcutaneous adipose tissue, partitioned by reticular, collagenous and elastic fibres. The subcutis of the canine footpads contains sweat glands embedded in the adipose tissue. The ducts of these glands channel through the thick epidermis of the foot pad. The secretions from these glands function as territorial or trail markers[MURDOCH:1334].
A ligament that supports a body part, especially an organ.
The cranial atrophic portion of the urogenital ridge attached to the cranial pole of the intraabdominal embryonic testis
The fetal ligament attached to the inferior end of the epididymis and testis and, at its other end, to the bottom of the scrotum; it is present during, and is thought to guide, the descent of the testis into the scrotum and then atrophies.
The upper part of the gubernaculum degenerates; The lower part persists as the gubernaculum testis ('scrotal ligament'). This ligament secures the testis to the most inferior portion of the scrotum, tethering it in place and limiting the degree to which the testis can move within the scrotum[WP]
A gubernaculum that is part of a female reproductive system.
The upper part of the gubernaculum, together with the ovarian artery and vein form the suspensory ligament of the ovary,[1] which suspends the ovary from the pelvic wall.; The lower gubernaculum has two vestigial remnants in females, the ovarian ligament and the round ligament of the uterus (ligamentum teres uteri) which respectively serve to support the ovaries and uterus in the pelvis
A ligament that does not connect two skeletal elements.
Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625].
this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus.
Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified].
logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://sourceforge.net/tracker/?group_id=76834&atid=1205376
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]
Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624].
A fibrous ligament that connects the ovary to the lateral surface of the uterus.
The ligament runs in the broad ligament of the uterus, which is a fold of peritoneum rather than a fibrous ligament. Specifically, it is located in the parametrium
Connects the cranial tip of the future gonad to the dorsocranial abdominal cavity.
TODO - check - add cranial ovarian susp ligaments
closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals
extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells
tissue that consists of two cellular layers (parietal endoderm and trophoblast) separated by a relatively thick nonvascular basement membrane (Reichert's membrane), and acts as a protective layer to supports and facilitates transport of nutrients between the uterine tissue and the yolk sac cavity.
The part of a molar tooth that is implanted in the gum; mandibular and maxillary molars usually have two and three roots, respectively.
A group of granular epithelial cells in the uterine muscle beneath the placenta that develops during pregnancy in rodents and some other species.
The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines
the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two
The middle layer of the muscularis; it is continuous with the circular layer of the esophagus, but is absent in the fundus and lies concentric to the longitudinal axis of the stomach; the circular layer is normally tonically constricted forming a functional pyloric sphincter, which controls the movement of chyme into the duodenum
This layer wraps in a circular orientation around the pylorus, and is held in a constricted state normally. The normal constriction of this muscle is what creates the pyloric sphincter, which controls the movement of chyme into the duodenum. This layer is concentric to the longitudinal axis of the stomach. (note: chyme is a thick and acidic mixture of acidic digestive fluids and partially digested food, which moves from the stomach to the small intestine as digestion moves along the digestive tract.)
FMA and MP disagree as to whether the circular layer is middle or innermost
stratum circulare (tunica muscularis)(gaster)
The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter
A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP]
The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands].
Kardong places this in the glandular epithelium, FMA more generally in the mucosa
Any of the branched tubular glands in the mucosa of the fundus and body of the stomach that secrete most of the digestive substances secreted by the stomach
The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP].
The innermost layer of the muscularis; it is not present in all sections of the stomach but is clearly seen in the fundus and near the lesser curvature of the corpus; the oblique fibers disappear distally (towards the pyloric antrum); the oblique layer is responsible for creating the motion that churns and physically breaks down the food
This layer is responsible for creating the motion that churns and physically breaks down the food. It is the only layer of the three which is not seen in other parts of the digestive system. The antrum has thicker skin cells in its walls and performs more forceful contractions than the fundus
FMA and MP disagree as to whether the oblique layer is middle or innermost. WP seems to agree that the oblique is inner
oblique fiber layer of gastric muscularis
The only layer of the three which is not seen in other parts of the digestive system[WP].
stomach smooth muscle inner oblique layer
The most superficial layer of the muscularis; it has two sections, a longitudinal layer that is common with the esophagus and ends in the corpus, and a longitudinal layer that originates in the corpus and spreads into the duodenum
longitudinal layer of gastric muscularis
outer longitudinal muscle layer of stomach
stratum longitudinale (tunica muscularis)(gaster)
stomach smooth muscle outer longitudinal layer
A transient cluster of cells in the central part of the dental epithelium facing the dental mesenchyme, which acts as an organizing center, providing positional information for tooth morphogenesis and regulating the growth of tooth cusps
The network of intersecting plates and spicules in cancellous bone which form a meshwork of intercommunicating spaces filled with blood vessels and marrow; in mature bone, the trabeculae are aligned in parallel with the lines of major compressive or tensile force
consider revision - we have 3 classes, the tissue itself, the network, and the spaces.
The distinguishing cell types of the lung alveolar tissue, including pulmonary epithelial cells (pneumocytes), alveolar capillary endothelial cells, interstitial cells (fibroblasts) and alveolar macrophages
The openings in the alveolar septum that permit air flow between adjacent alveoli
The part of the airway consisting of a respiratory bronchiole and all of its branches
Any skeletal muscle organ in the hypodermis / superficial fascia
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
The multi-layer basement membrane between the dermis and epidermis that serves to adhere the dermis and epidermis, provide mechanical support for the epidermis, and forms a barrier to cells and large molecules across the junction
subclasses (anterior, superior, posterior) can be added on request
Unique telencephalic subventricular zones that extend from the lateral ventricles into the olfactory bulbs. Newly produced GABAergic interneurons migrate along the RMS and settle in the bulb.
The rostral migratory stream (RMS) or rostral migratory pathway is a pathway, found in the brain of some animals, along which neuronal precursors that originated in the subventricular zone (SVZ) of the brain migrate to reach the main olfactory bulb, where they differentiate into interneurons. Neurogenesis has been shown to occur in the SVZ into adulthood[WP]
The transient structure formed by neurons migrating from the subventricular zone into the olfactory bulb[MP:0004279]s
In rodents, the anterior region of the SVZ produces neuroblasts that migrate in chain toward the olfactory bulb along the so-called rostral migratory stream (RMS)
The nerve fiber tracts that span the midline of the spinal cord
Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.
Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO]
Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n
Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA.
A putamen that is part of a left cerebral hemisphere.
A putamen that is part of a right cerebral hemisphere.
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus.
The vesical plexus envelops the lower part of the bladder and the base of the prostate and communicates with the pudendal and prostatic plexuses. It is drained, by means of several vesical veins, into the hypogastric veins.
The uterine plexuses lie along the sides and superior angles of the uterus between the two layers of the broad ligament, and communicate with the ovarian and vaginal plexuses. They are drained by a pair of uterine veins on either side: these arise from the lower part of the plexuses, opposite the external orifice of the uterus, and open into the corresponding hypogastric vein.
External gills are the gills of an animal, most typically an amphibian, that are exposed to the environment, rather than set inside the pharynx and covered by gill slits, as they are in most fishes[BTO].
External gills are the gills of an animal, most typically an amphibian, that are exposed to the environment, rather than set inside the pharynx and covered by gill slits, as they are in most fishes. Instead, the respiratory organs are set on a frill of stalks protruding from the sides of an animals head. This type of gill is most commonly observed on the aquatic larva of most species of salamanders, lungfish, and bichirs (which have only one large pair), and are retained by neotenic adult salamanders and some species of adult lungfish. They are present on non-transforming salamander species such as the mudpuppy, as well as most members of the Proteidae and Sirenidae families, which naturally never metamorphose into an air-breathing form. The embryos of frogs and caecilians also develop external gills at some point in their development, though these are either resorbed before or disappear shortly after hatching. Fossils of the distant relatives of modern amphibians, such as Branchiosaurus and Apateon, also show evidence of external gills. The external gills commonly consist of a single stalk (rami) protruding from a gill arch behind the head of the animal, above an associated gill slit. The stalk usually contains muscle tissue, and may be moved by the animal as a free appendage, in order to stir up stagnant water. The stalk is lined by many thinly walled filaments (fimbriae), containing the majority of blood vessels used in gas exchange. Animals usually have one external gill originating on each gill arch (except the hyoid), which leads to there being three pairs of external gills in salamanders, and four in the gilled larvae of lungfish[Wikipedia:External_gills].
A primordium or bud that develops into a gill.
Subdivision of endoskeleton derived from pharyngeal arches
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher.
Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO]
An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO].
Surface structure involved in locomotion.[TAO]
Surface structure involved in locomotion.[VSAO]
This class groups together various structures that may have arisen through convergent evolution, including, for example, the dorsal fin of a cetacean
Lateral protrusion of the third ventricle.
lateral recess of diencephalic ventricle
Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements.
Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO]
Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]
relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO]
relationship loss: subclass lateral line receptor (AAO:0010705)[AAO]
Cranial nerves that carry afferent and efferent fibers for the lateral line system.
Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO]
relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO]
relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO]
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
Bone element that is adjacent to the notochord.
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
Replacement bone that forms within or surrounding a cartilaginous skeletal element.
This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
Bone element that is located on the surface of a cartilage element.
Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]
include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
An anatomical space that is an opening, usually at the end of a canal or duct, on the surface of the integument or the lining of an internal anatomical space.
Organ that consists of receptor cells located within an epidermal invagination and functions as an electroreceptor.
An electroreceptor consisting of receptor cells sunk into the epidermis or located in an epidermal cavity opening to the surface through a duct and pore. It can detect weak electric currents generated by other animals.[AAO]
relationship loss: subclass lateral line receptor organ (AAO:0001001)[AAO]
The ampullae of Lorenzini are special sensing organs called electroreceptors, forming a network of jelly-filled pores. Each ampulla consists of a canal opening to the surface by a pore in the skin and ending blindly in a cluster of small pockets full of special jelly. The ampullae are mostly clustered into groups inside the body, each cluster having ampullae connecting with different parts of the skin, but preserving a left-right symmetry. The canal lengths vary from animal to animal, but the distribution of the pores is generally specific to each species. The ampullae pores are plainly visible as dark spots in the skin. They provide fish with a sixth sense capable of detecting electromagnetic fields as well as temperature gradients[WP].
obsolete mesenchyme from splanchnopleure
A retinal neural layer that is immediately adjacent to the inner nuclear layer and comprises 20 percent of the inner plexiform layer of retina.
A retinal neural layer that is immediately adjacent to the S1 and S3 layers and comprises 20 percent of the inner plexiform layer of retina.
A retinal neural layer that is immediately adjacent to the S2 and S4 layers and comprises 20 percent of the inner plexiform layer of retina.
A retinal neural layer that is immediately adjacent to the S3 and S5 layer and comprises 20 percent of the inner plexiform layer of retina.
A retinal neural layer that is immediately adjacent to the retinal ganglion cell layer and comprises 20 percent of the ganglion plexiform layer of retina.
Area of the parietal lobe concerned with receiving general sensations. It lies posterior to the central sulcus.
TODO - add relationship to system (not part of, as sensory systems are peripheral)
(Chapin & Lin, 1984, rat): the region considered as the SI cortex is not a cytoarchitecturally homogeneous structure but consists instead of a patchwork array of areas containing dense aggregations of layer IV granule cells, surrounded by granule-cell-sparse regions. As was shown by Welker (b71,b76), and in our own mapping studies (see Fig. 3), this discontinuous pattern of granular, or koniocortical, zones contains within itself a map of the ratbs cutaneous periphery. There are clear subtypes within this cytoarchitectural subregion, notably including the bgranular aggregateb type of cytoarchitecture characteristic of the paw, limb, and mystacial vibrissae areas, and the bbarrel-fieldb type (originally described by Woolsey and Van der Loos, b70) seen in the nose and perioral regions. In the mouse, but not the rat, such barrels also cover the whole whisker representation (Welker and Woolsey, b74).
ABA disjointness - Removed relationship: part_of UBERON:0001870 frontal cortex
the area of the upper bank of the lateral sulcus that is involved in somatic sensation
The posterior oviduct opens into the large white albumen gland which adds a layer of albumen to the zygote before it reaches the egg capsule gland.
A small opening on the side of the head in some gastropods through which the penis is protruded.
Mollusks have three distinct divisions of their body. The head contains the sensory equipment (eyes, antennae, etc) and the primitive brain. The visceral hump, which is the main body, contains most of the organs, including a complete digestive and excretory tract as well as the reproductive organs. The visceral hump also includes the two external flaps of tissue, which are known as the mantle.
The pedal ganglia mainly are necessary for coordination of locomotion of a snail.
A lateral ganglion that innervates pallial cavity, gills and skin of a snail[BTO,modified].
A knot of nerves in The pallial cavity that innervates the mantle of a snail[BTO,modified].
The cerebral ganglia are primarily sensual centres, that compute information from the eyes as well as from the tactile and position sensors (statocystes). Besides coordination they also serve the locational memory of a snail.
The head-foot is the part you see most easily in slugs and snails. It is mostly a muscular organ covered in cilia and rich in mucous cells, which the mollusc uses to move around, it normally tapers to a tail at one end and has a head incorporated in the front. The head includes a mouth, eyes and tentacles, the last two may be much reduced or even absent. In those species with shells the head-foot can be drawn into the shell.
Albumen is the clear liquid contained within an egg and consists of water and proteins, among which are ovomucin and ovomucoid. It protects the egg yolk and provides additional nutrition for the growth of the embryo.
An extraembryonic epithelium that is formed by the delaminated cells of the primitive endoderm (hypoblast) that goes on to form the yolk sac. In mammals, as in avians, these cells do not produce any part of the newborn organism (i.e. they are extraembryonic)
The origin of extraembryonic endoderm is a highly controversial issue
A lobe of the lung that is closest to the head.
the logical definition must have a clause stating position relative to a lower lobe, otherwise a single lobed side (such as the left lobe in the mouse) trivially classifies as an upper lobe
The bottom most subdivision of either the right or left lung.
The azygous lobe of the lung is an accessory lobe of the right lung. It is rare and usually associated with an abnormality of the azygous vein. It is produced by an aberrant position of the azygous vein near the hilum of the lung. It divides the right superior lobe near the apex of the lung down to the hilum in roughly the median plane. The fissure created, the meso-azygous fissure, is lined by both visceral and parietal pleura. The lobe lies superomedial to the fissure.
A lobe of lung that is part of a left lung.
1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure
The lobe of the left lung that is closest to the head.
A lower lobe of lung that is part of a left lung.
Anterioinferior portion of left upper lung lobe
the lingula of the left lung in humans is not normally considered a true lobe
A lobe of the lung that is situated somewhere between an upper lobe and lower lobe.
mice have 4 right lobes (5 in some schemes), humans have 2, and thus no middle lobe (the lingula is not a lobe)
A layer of new bone growth outside existing bone seen in pyogenic osteomyelitis. It results from the stripping off of the periosteum by the accumulation of pus within the bone, and new bone growing from the periosteum.
A piece of dead bone that has become separated during the process of necrosis from normal/sound bone..
A hollow bony structure on the ventral, posterior portion of the skull of placental mammals that encloses parts of the middle and inner ear. In most species, it is formed by the tympanic part of the temporal bone.
In extant primates, the structure is found in tarsiers, lemurs, and lorises[WP]. When present in marsupials, it usually forms the alisphenoid; in placentals variously constructed of ectotympanic, entotympanic, petrosal, or a combination of these and others
may be formed from entotympanic and ectotympanic
The melon is an ovoid-shaped, fatty organ found in the forehead of all toothed whales (odontocetes), including dolphins and porpoises (Cranford et al., 1996; Harper, C. J., et al., 2008) and believed to be used in echolocation
A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder.
The tip of a toe of an ungulate mammal, strengthened by a thick horny (keratin) covering. The hoof consists of a hard or rubbery sole, and a hard wall formed by a thick nail rolled around the tip of the toe. The weight of the animal is normally borne by both the sole and the edge of the hoof wall. Hooves grow continuously, and are constantly worn down by use.
The hoof is the integument of the foot. Like skin, the integument of the foot has three layers, namely the epidermis, dermis, and SC tissue.
An unpaired knot of nerves in The visceral sacs that innervates the pallial organs as well as the inner organs.
The semioval center is the white matter found underneath the grey matter on the surface of the cerebrum. The term is synonymous with cerebral white matter. The white matter, located in each hemisphere between the cerebral cortex and nuclei, as a whole has a semioval shape. It consists of cortical projection fibers, association fibers and cortical fibers.
WP suggests a merge with cerebral white matter
The dental follicle is a sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively.
The distal portion of the colon; it develops embryonically from the hindgut and functions in the storage and elimination of waste.
The proximal portion of the colon, extending from the ileocecal valve usually to a point proximal to the left colic flexure; it develops embryonically from the terminal portion of the midgut and functions in absorption.
A gland whose discharged secretion contains part of the secreting cells.
A gland in the posterior expansion of the oviduct that secretes the calcareous surroundings of the egg shell.
The venom gland of snakes is in actual fact a modified salivary gland and is linked to the groove in the fangs by a duct.
snake venom glands are modified salivary glands. In future this class may be merged into a more general modified salivary gland venom gland class
The pes anserinus is the insertion of the conjoined tendons of three muscles onto the anteromedial (front and inside) surface of the proximal extremity of the tibia.
Consider adding muscle insertion site class
In carnivores, either of two sacs found between the internal and external anal sphincters, lined with sebaceous glands and in some species with apocrine glands.
The olfactory region of the brain, located in the cerebrum.
Obsoleted because The term rhinencephalon has been used to describe different structures at different points in time.[ISBN 0-8493-8631-4]. May refer to: a specific structure in aves; a part of the brain involved with olfaction;
A dense regular connective tissue that that connects muscles together[WP, modified].
The functional tissue of the kidney, consisting of the nephrons.
One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed.
The part of the chorion where the villi persist, forming the foetal part of the placenta.
The gray matter of the habenula, composed of a small-celled medial and a larger-celled lateral habenular nucleus; both nuclei receive fibres from basal forebrain regions (septum, basal nucleus, lateral preoptic nucleus); the lateral habenular nucleus receives an additional projection from the medial segment of the globus pallidus. Both nuclei project by way of the retroflex fasciculus to the interpeduncular nucleus and a medial zone of the midbrain tegmentum.
Stomach found in horses; includes cardiac, proper gastric and pyloric glandular zones.
We have a distinct class for 'glandular region of stomach'. We may want to merge into this class, even though this is not considered a distinct stomach.
Four accumulations of gray substance embedded in the white substance of the cerebellum, comprising the nucleus dentatus, nucleus emboliformis, nucleus globosus, and nucleus fastigii.
System pertaining to blood vessels in the brain.
The tissues which attach the third phalanx to the hoof wall.
A bony process projecting backward and medialward from the posterior border of the ischium.
From the posterior border of the body of the Ischium there extends backward a thin and pointed triangular eminence, the ischial spine, more or less elongated in different subjects. It can serve as a landmark in pudendal anesthesia[Wikipedia:Ischial_spine].
The membrane separating the fetal from the maternal blood in the placenta.
One of the two primary bendings of a typical leg, pertains to the femur and the tibia.
proposed OWL definition: skeletal join that connects ONLY tibia and femur
One of several small inconstant lymph nodes, proximal, intermediate and distal deep to the fascia lata and medial to the femoral vein; they receive lymph from the deep structures of the lower limb, from the glans penis and from superficial inguinal nodes; efferents pass to the external iliac nodes.
A group of 12-20 lymph nodes that lie in the subcutaneous tissue below the inguinal ligament and along the terminal part of the great saphenous vein; they drain the skin and subcutaneous tissue of the lower abdominal wall, perineum, buttocks, external genitalia, and lower limbs.
nodus lymphaticus inguinalis superficialis
Carotid branch of glossopharyngeal nerve.
fibrocartilage in which strong bundles of white fibrous tissue predominate.
A zone of skin that is part of a lower back.
A zone of skin that is part of a dorsal thoracic segment of trunk.
An uterine horn that is in the left side of a uterus.
An uterine horn that is in the right side of a uterus.
A transient cortical layer juxtaposed to the medulla and the zona reticularis; in males, this zone rapidly involutes at the onset of puberty whereas this zone persists in females until the first pregnancy or later in adulthood in non-pregnant females
Abdominal artery that follows the curvature of the stomach. The right gasteroepiploic artery is frequently used in coronary artery bypass grafting, myocardial revascularization, and other vascular reconstruction.
One of two (deep circumflex and superficial circumflex) iliac arteries that supply the lower abdomen, inguinal lymph nodes, sartorius, and tensor fasciae latae.
An artery that supplies blood to the urinary bladder.
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
An organ part that is part of a stomach.
Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.
The groove on the external surface of the ampulla of each semicircular duct where the nerve enters the ampullary crest.
A germinal center that is located in a lymph node
The deep circumflex iliac artery (or deep iliac circumflex artery) is an artery in the pelvis that travels along the iliac crest of the pelvic bone.
The superficial iliac circumflex artery (or superficial circumflex iliac), the smallest of the cutaneous branches of the femoral artery, arises close to the superficial epigastric artery, and, piercing the fascia lata, runs lateralward, parallel with the inguinal ligament, as far as the crest of the ilium. It divides into branches which supply the integument of the groin, the superficial fascia, and the superficial subinguinal lymph glands, anastomosing with the deep iliac circumflex, the superior gluteal and lateral femoral circumflex arteries.
The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses.
The pudendal plexus (vesicoprostatic plexus) lies behind the arcuate pubic ligament and the lower part of the pubic symphysis, and in front of the bladder and prostate. Its chief tributary is the deep dorsal vein of the penis, but it also receives branches from the front of the bladder and prostate. It communicates with the vesical plexus and with the internal pudendal vein and drains into the vesical and hypogastric veins.
A neural nucleus that is part of the solitary tract nuclear complex. The solitary tract and nucleus are structures in the brainstem that carry and receive visceral sensation and taste from the facial (VII), glossopharyngeal (IX) and vagus (X) cranial nerves. [WP,unvetted].
nucleus tractus solitarii medullae oblongatae
merge with SOC? See https://github.com/obophenotype/uberon/issues/631#issuecomment-67754754
The Open Circulatory System is a system in which fluid (called hemolymph) in a cavity called the hemocoel bathes the organs directly with oxygen and nutrients and there is no distinction between blood and interstitial fluid; this combined fluid is called hemolymph or haemolymph
consider merging with cardiovascular system?
The circulatory systems of all vertebrates, as well as of annelids (for example, earthworms) and cephalopods (squid and octopus) are closed, just as in humans. Still, the systems of fish, amphibians, reptiles, and birds show various stages of the evolution of the circulatory system
A closed circulatory system in which blood passes twice through the heart to supply the body once.
A closed circulatory system in which blood passes once through the heart to supply the body once.
A bellows-shaped respiratory unit extending from the outer wall of the lung into a central air space.
Dunker (1978) coined the terms ediculae or faveoli to describe the unit structure of the reptilian parenchymal, which are analogous to mammalian alveoli, but are up to 1,000 times larger than alveoli of similar sized mammals[PMID:12625309]
Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs
Three distinct sets of organs perform respiration—the anterior air sacs (interclavicular, cervicals, and anterior thoracics), the lungs, and the posterior air sacs (posterior thoracics and abdominals). The posterior and anterior air sacs, typically nine, expand during inhalation. Air enters the bird via the trachea. Half of the inhaled air enters the posterior air sacs, the other half passes through the lungs and into the anterior air sacs. Air from the anterior air sacs empties directly into the trachea and out the bird's mouth or nares. The posterior air sacs empty their air into the lungs. Air passing through the lungs as the bird exhales is expelled via the trachea. Some taxonomic groups (Passeriformes) possess 7 air sacs, as the clavicular air sacs may interconnect or be fused with the cranial thoracic air sacs[WP]
interclavicular, cervicals, & anterior thoracics
Half of the inhaled air enters the posterior air sacs. The posterior air sacs empty their air into the lungs. // posterior thoracics & abdominals
vocal organ of birds, located at the base of a trachea
A anatomical wall that is part of a syrinx organ.
A delicate bar of cartilage connecting the dorsal and ventral extremities of the first pair of bronchial cartilages in the syrinx of birds
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb
inner medulla vasa recta descending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb
outer medulla vasa recta descending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb
Obsoleted as the gravid stage is not a life cycle stage. A similar term may be recreated when we have stages specific to structures such as the uterus
An organism containing a developing embryo, fetus, or unborn offspring within the body.
An invagination of the intestinal epithelium that emanates from a lamina of mesenchymal cells located between the dorsal aorta and the upper intestine and constitute one of the two principal hematopoietic organs at the ammocoete stage of development.
Lymphocytes are also abundant in the lamprey kidney, where large populations are intermingled around the renal tubules
One of the primary immunological organs of the adult lamprey is the supraneural body. This structure lies dorsal to spinal column and becomes heavily populated with lymphocytes following after immune challenge [13–15]. The supraneural body from hematopoietically stimulated lampreys appears to be histologically-similar to ‘bone marrow’ in higher vertebrates and contains all blood cell lineages and their precursors, including lymphocytes at all stages of maturity[16].
A mature thymus that is entirely part of the cervical region.
A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN-10:0781714125]
A mature thymus that is entirely part of thoracic region.
A thymus-like lympho-epithelial structures, in the tips of the gill filaments and the neighbouring secondary lamellae (both within the gill basket) of lamprey larvae.
A gonad prior to differentiating into a definitive testis or ovary.
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
The network-like cartilaginous skeleton of the gill region of Petromyzontiformes and Holocephali
developmental relationship needs to be changed if the scope is broadened, as NC is vertebrate-specific
Portion of tissue that projects outward from the gill and is a thread-like, soft, red respiratory and excretory structure.
Branched region of the gill where respiratory exchange takes place. Kimmel et al, 1995.[TAO]
Nerve carrying fibers from the vomeronasal organ epithelium to the accessory olfactory bulb.
Nerve carrying fibers from the vomeronasal organ to the accessory olfactory bulb.[AAO]
In the human this disappears before birth
accessory olfactory bulb vomeronasal nerve
The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary
consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm
Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke’s pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke’s pouch, the anlage of the adenohypophysis. Rathke’s pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke’s pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)
Rostralmost epibranchial placode. Associated with 1st branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion
Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion
Caudalmost epibranchial placode. Associated with 3rd branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: Gives rise to inferior vagus ganglion. Note that ZFA has 4 vagal placodes
Cranial ganglion which develops from an epibranchial placode.
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
Specialized series of dorsolateral ectodermal placodes.[AAO]
An endocardium that is part of a right atrium.
Obsoleted as the meaning of the class was unclear in earlier versions of EHDAA2
One of a group of three muscles fibularis (peronæus) longus, brevis, and tertius originating on the fibula and inserting on the metatarsals
A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities.
only a vestige of the right duct in the adult hagfish (21)[PMID:20959416, S1]
A posterior cardinal vein that is in_the_right_side_of a multicellular organism.
A subcardinal vein that is in_the_right_side_of a multicellular organism.
A vein that is part of a craniocervical region.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
opening in the septum primum between the two atria of the embryonic heart[TMD].
First of the two openings to perforate the septum primum between the two atria of the embryonic heart. [TFD][VHOG]
A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation.
sphenoid bone pre-cartilage condensation
basi-sphenoid pre-cartilage condensation
A sphenoid endochondral element that is composed primarily of a cartilage tissue.
The dorsal part of the cloacal membrane following its partition by the urorectal septum.
A basioccipital endochondral element that is composed primarily of a pre-cartilage condensation.
basioccipital pre-cartilage condensation
Any suture between cranial and/or facial bones.
we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA
The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium.
A nephric duct is a tube that drains a primitive kidney[GO].
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb
Mesenchyme that is part of a medial nasal prominence.
Mesenchyme that is part of a lateral nasal prominence.
An ectoderm that is part of a lateral nasal prominence.
Area on the rostral portion of the soft palate rich in tastebuds (Miller and Spangler 1982).
A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo.
In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG]
each membrane is initially composed of an inner layer formed by the endodermal lining of a branchial pouch and an outer layer formed by the ectodermal lining of the branchial groove; later, these two layers become separated by a thin layer of mesoderm; only the first branchial membrane contributes to the formation of an adult structure, i.e. the tympanic membrane (aka eardrum); the second, third, and fourth membranes are obliterated[MP]
A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch.
check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches
A pharyngeal membrane that separates the second pharyngeal cleft from the second pharyngeal pouch.
A pharyngeal membrane that separates the third pharyngeal cleft from the third pharyngeal pouch.
A pharyngeal membrane that separates the fourth pharyngeal cleft from the fourth pharyngeal pouch.
A vertebral centrum element that is composed primarily of a cartilage tissue.
cartilaginous centrum of vertebra[PMID:11746457]
medial or lateral; in EHDAA2 also frontonasal or intermaxillary
A small bone in the fetus between the basilar process and the basisphenoid.
The posterior portion of the sphenoid bone developed in five separate parts consisting of a central basisphenoid, the two alisphenoids, and the two medial pterygoid laminae.
The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis).
The axilla is the area directly under the joint where the forelimb connects to the shoulder.
either of a pair of fleshy lateral processes borne by most segments of a polychaete worm.
The madreporite is an opening used to filter water into the water vascular system of echinoderms. It is visible as a small red or yellow button-like structure, looking like a small wart, on the aboral surface of the central disk of a sea star. Close up, it is visibly structured, resembling a 'madrepore' colony. From this, it derives its name. The water vascular system of the sea star consists of a series of seawater-filled ducts that function in locomotion and feeding and respiration. Its main parts are the madreporite, the stone canal, the ring canal, the radial canals, the lateral canals, and the tube feet. The sieve-like madreporite allows entry of seawater into the stone canal, which connects to the ring canal around the mouth. Five or more radial canals extend from the ring canal, one in each arm above the ambulacral groove. From the radial canals extend many lateral canals, each of which leads to a tube foot. Each tube foot is a closed cylinder with muscular walls, having a sucker at the outer end and a bulb-like ampulla at its inner end within the body cavity.
Mesenchyme that is part of a otic placode.
Mesenchyme that is part of a developing midgut.
previously logically defined as mesenchyme of midgut, but this caused disjointness violations between dense and loose mesenchyme
An ectoderm that is part of a buccopharyngeal membrane.
An endoderm that is part of a buccopharyngeal membrane.
A tube lumen that is part of a pericardio-peritoneal canal.
cavity of the pericardio-peritoneal canal
Mesenchyme that is part of a foregut-midgut junction.
associated mesenchyme of foregut-midgut junction
A mesentery that is part of a foregut-midgut junction.
dorsal mesentery of mesentery of foregut-midgut junction
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
An epithelium that is part of a foregut-midgut junction.
parietal of mesothelium of pericardio-peritoneal canal
Mesenchyme that is part of a ear vesicle.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head
ventral mesentery of mesentery of foregut-midgut junction
Mesenchyme that is part of a developing hindgut.
Mesenchyme that is part of a developing main bronchus.
Mesenchyme that is part of a developing trachea.
Mesenchyme that is part of a developing middle ear.
Also 1st arch maxillary mesenchyme in EHDAA2
An endoderm that is part of a anal region.
An epithelium that is part of a lateral lingual swelling.
Mesenchyme that is part of a maxillary prominence.
A vascular plexus that is part of a left lung.
A vascular plexus that is part of a right lung.
Mesenchyme that is part of a sublingual gland primordium.
mesenchyme of sublingual gland primordium
Mesenchyme that is part of a submandibular gland primordium.
submaxillary gland primordium mesenchyme
mesenchyme of submandibular gland primordium
A hepatic sinusoid that is part of a left lobe of liver.
hepatic sinusoid of left of lobe of liver
A hepatic sinusoid that is part of a right lobe of liver.
hepatic sinusoid of right of lobe of liver
An endoderm that is part of a foregut-midgut junction.
A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium).
Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2–3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults
A segment of the manual digit containing the distal phalanx
A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone.
The bottommost bone in the equine leg and is encased by the hoof capsule. The distal phalanx articulates with both the middle phalanx and the distal sesamoid, forming the distal interphalangeal joint
Was made obsolete in favor of the more generic grouping
The middle phalanx of digit 3 in a horse
in future this may be merged into a species-neutral phalanx 2 digit III
The proximal phalanx of digit 3 in a horse
in future this may be merged into a species-neutral phalanx 1 digit III
A bone that is part of the pastern region of a horse limb. i.e. proximal or middle (P1 or P2) phalanges in digit 3.
in future this may be merged into a more species-neutral class
A skeletal joint that connects a mesopodium bone and connects a proximal phalanx.
We include these joints as being part of the digits; this is consistent with the FMA, and makes classification easier. Note that digit and metapodial regions are part-disjoint
A part of the leg of a horse between the fetlock and the top of the hoof. It incorporates the long pastern bone (proximal phalanx) and the short pastern bone (middle phalanx), which are held together by two sets of paired ligaments to form the pastern joint (proximal interphalangeal joint)
in future this may be merged into a more species-neutral class for the distal and medial segments of a digit.
A submucosa that is part of a intestine.
Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions.
thoracolumbar region of vertebral column
A sulcus limitans of neural tube that is part of a future spinal cord.
spinal cord lateral wall sulcus limitans
In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate.
A cerebrospinal fluid-filled space that runs longitudinally through the length of the entire spinal cord. The central canal is contiguous with the ventricular system of the brain. The central canal represents the adult remainder of the neural tube.
In the floor of the fourth ventricle, the sulcus limitans separates the cranial nerve motor nuclei (medial) from the sensory nuclei (lateral). In the superior part of the rhomboid fossa, it corresponds with the lateral limit of the fossa and presents a bluish-gray area, the locus ceruleus (which owes its color to an underlying patch of deeply pigmented nerve cells, termed the substantia ferruginea). [WP]
A sulcus limitans of neural tube that is part of a future medulla oblongata.
A sulcus limitans of neural tube that is part of a future metencephalon.
A sulcus limitans of neural tube that is part of a future myelencephalon.
The ventral half of the developing neural tube that is the myelencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
Mesenchyme that is part of a 1st arch mandibular component.
mesenchymal region of mandibular component of first pharyngeal arch
Mesenchyme that is part of a developing interdigital region.
influences identity of anterior digit[Dahn and Fallon 2000], likely via BMP4
An interdigital region mesenchyme that is part of a interdigital region between manual digits 1 and 2.
interdigital region between fingers 1 and 2 mesenchyme
mesenchyme of interdigital region between manual digits I and II
mesenchyme of interdigital region between manual digits 1 and 2
An interdigital region mesenchyme that is part of a interdigital region between manual digits 2 and 3.
interdigital region between fingers 2 and 3 mesenchyme
mesenchyme of interdigital region between manual digits II and III
mesenchyme of interdigital region between manual digits 2 and 3
An interdigital region mesenchyme that is part of a interdigital region between manual digits 3 and 4.
interdigital region between fingers 3 and 4 mesenchyme
mesenchyme of interdigital region between manual digits III and IV
mesenchyme of interdigital region between manual digits 3 and 4
An interdigital region mesenchyme that is part of a interdigital region between manual digits 4 and 5.
interdigital region between fingers 4 and 5 mesenchyme
mesenchyme of interdigital region between manual digits IV and V
mesenchyme of interdigital region between manual digits 4 and 5
An interdigital region mesenchyme that is part of a interdigital region between pedal digits 1 and 2.
interdigital region between toes 1 and 2 mesenchyme
mesenchyme of interdigital region between pedal digits I and II
mesenchyme of interdigital region between pedal digits 1 and 2
An interdigital region mesenchyme that is part of a interdigital region between pedal digits 2 and 3.
interdigital region between toes 2 and 3 mesenchyme
mesenchyme of interdigital region between pedal digits II and III
mesenchyme of interdigital region between pedal digits 2 and 3
An interdigital region mesenchyme that is part of a interdigital region between pedal digits 3 and 4.
interdigital region between toes 3 and 4 mesenchyme
mesenchyme of interdigital region between pedal digits III and IV
mesenchyme of interdigital region between pedal digits 3 and 4
An interdigital region mesenchyme that is part of a interdigital region between pedal digits 4 and 5.
interdigital region between toes 4 and 5 mesenchyme
mesenchyme of interdigital region between pedal digits IV and V
mesenchyme of interdigital region between pedal digits 4 and 5
An interdigital region mesenchyme that is part of a interdigital region between digits 1 and 2.
mesenchyme of interdigital region between digits I and II
mesenchyme of interdigital region between digits 1 and 2
An interdigital region mesenchyme that is part of a interdigital region between digits 2 and 3.
mesenchyme of interdigital region between digits II and III
mesenchyme of interdigital region between digits 2 and 3
An interdigital region mesenchyme that is part of a interdigital region between digits 3 and 4.
mesenchyme of interdigital region between digits III and IV
mesenchyme of interdigital region between digits 3 and 4
An interdigital region mesenchyme that is part of a interdigital region between digits 4 and 5.
mesenchyme of interdigital region between digits IV and V
mesenchyme of interdigital region between digits 4 and 5
An interdigital region mesenchyme that is part of a manus.
mesenchyme of interdigital region of forelimb
mesenchyme of interdigital region of manus
An interdigital region mesenchyme that is part of a pes.
mesenchyme of interdigital region of hindlimb
mesenchyme of interdigital region of pes
Mesenchyme that is part of a developing left lung.
Mesenchyme that is part of a developing right lung.
A neural plate that develops_from a future forebrain.
A neural plate that develops_from a presumptive midbrain.
forebrain midbrain boundary neural plate
A neural plate that develops_from a presumptive hindbrain.
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
midbrain hindbrain boundary neural plate
A presumptive structure that has_potential_to_develop_into a midbrain.
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
A proximal straight tubule that is part of a pronephros.
The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule.
ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS)
The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions.
The five sacral nerves emerge from the sacrum. Although the vertebral components of the sacrum are fused into a single bone, the sacral vertebrae are still used to number the sacral nerves. Posteriorly, they emerge from the posterior sacral foramina, and form the posterior branches of sacral nerves. Anteriorly, they emerge from the anterior sacral foramina, and contribute to the sacral plexus (S1-S4) and coccygeal plexus.
The coccygeal nerve is the spinal nerve that corresponds to the coccyx bone.
A spinal nerve root that is part of a thoracic nerve.
A spinal nerve root that is part of a lumbar nerve.
A spinal nerve root that is part of a sacral nerve.
A spinal nerve root that is part of a coccygeal nerve.
Chondrocranium chondrification center that fuses with cartilages derived from sclerotome region of occipital somites forming occipital bone, hypoglossal canals and foramen magnum.
Rod-shaped paired cartilages on either side of the notochord. They unite, forming the base of the chondrocranium and are replaced by the prootic bones.[TAO]
Chondrocranium chondrification center that that forms anterior body of sphenoid, containing the sella turcica and posterior body of sphenoid.
classified as part of chondrocranium based on developmental relationships
merge with sphenoid lesser wing cartilage element?
The body of the sphenoid bone, more or less cubical in shape, is hollowed out in its interior to form two large cavities, the sphenoidal air sinuses, which are separated from each other by a septum.
forms around the developing pituitary, and together with prechordal cartilages creates body of sphenoid bone
The ansa lenticularis (ansa lentiformis in older texts) is a part of the brain, making up the superior layer of the substantia innominata of Meynert. Its fibers, derived from the medullary lamina of the lentiform nucleus, pass medially to end in the thalamus and subthalamic region, while others are said to end in the tegmentum and red nucleus. It is classified by NeuroNames as part of the subthalamus.
ventral peduncle of lateral forebrain bundle
A pathway containing fibers from midbrain nuclei that project to the inferior olivary complex, as well as fibers originating in the pontine reticular formation and the medullary reticular formation that project to several nuclei of the thalamus. It can be identified in the midbrain and the pons (Adapted from Brain Info).
The central tegmental tract is a structure in the midbrain and pons. The central tegmental tract includes ascending axonal fibers which arise from the rostral nucleus solitarius and terminate in the ventral posteromedial nucleus (VPM) of thalamus. Information from the thalamus will go to cortical taste area, namely the insula and frontal operculum. It also contains descending axonal fibers from the parvocellular red nucleus. The descending axons will project to the inferior olivary nucleus. This latter pathway will be used to connect the contralateral cerebellum[Wikipedia:Central_tegmental_tract].
A paired accessory, glandular, androgen-dependent outpouchings of the proximal ductus deferens, one on each side, that produce and secrete lipids and glycogen, components of the seminal fluid; they open into the ampullae at the level of the colliculus seminalis, are lined by simple columnar epithelium with large, oval nuclei, and may be distinguished from those of the prostate as they are surrounded by a characteristic, dense, fibromuscular stroma
Ampullary glands are situated in an ampulla-like enlargement of the seminal duct, or embedded in the latter; they are present, eg in the Shrew, Ruminants, and certain Carnivores and Rodents. (Wiedersheim et al., 1907)
there is no known human counterpart to the ampullary glands of the mouse[MP]
usually encapsulated by connective tissue and containing smooth muscle
A sympathetic nerve trunk that is part of a lower back.
One of the two epithelia which make up the tympanic membrane (along with the fibrous layer)
A eyelid connective tissue that is part of a hypodermis.
The portions of renal substance (cortex) intervening between the bases of the pyramids and the capsule of the kidney.
A basement membrane that is part of a nephron tubule.
A basement membrane that is part of a bronchus.
A basement membrane that is part of a trachea.
A branch of the maxillary artery that is found in the gingiva, premolars, and molars.
An artery that supplies oxygenated blood to the ear.
A branch of the abdominal aorta that supplies oxygenated blood to the testis.
add child terms; consider merging with testicular artery
A nucleus of brain that is part of a telencephalon.
An anatomical space that surrounded_by a embryonic cloaca.
An anatomical space that surrounded_by a rectum.
The nasal fin is an epithelial seam that develops by fusion between the epithelial linings of the medial and lateral nasal swellings. Shortly after its formation the nasal fin regresses and is replaced by mesenchyme, with exception of its most posterior portion which remains as the bucconasal membrane.
The oronasal membrane separates the oral cavity and nasal cavity.
May be obsoleted in future. WP states: Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] But because the cranial component rapidly joins the vagus nerve and serves the same function as other vagal nerve fibers, modern descriptions often consider the cranial component part of the vagus nerve and not part of the accessory nerve proper.
Thus in contemporary discussions of the accessory nerve, the common practice is to dismiss the cranial part altogether, referring to the accessory nerve specifically as the spinal accessory nerve.
The chorda tympani is a nerve that branches from the facial nerve (cranial nerve VII) inside the facial canal, just before the facial nerve exits the skull via the stylomastoid foramen. Chorda tympani is a branch of the facial nerve (the seventh cranial nerve) that serves the taste buds in the front of the tongue, runs through the middle ear, and carries taste messages to the brain. The chorda tympani is part of one of three cranial nerves that are involved in taste. The taste system involves a complicated feedback loop, with each nerve acting to inhibit the signals of other nerves. The chorda tympani appears to exert a particularly strong inhibitory influence on other taste nerves, as well as on pain fibers in the tongue. When the chorda tympani is damaged, its inhibitory function is disrupted, leading to less inhibited activity in the other nerves.
parasympathetic root of submandibular ganglion
radix parasympathica ganglii submandibularis
Anatomical cluster consisting of adjacent teeth constituting a row.
A tooth row that is part of a skeleton of lower jaw.
A tooth row that is part of a skeleton of upper jaw.
The middle cardiac vein commences at the apex of the heart, ascends in the posterior longitudinal sulcus, and ends in the coronary sinus near its right extremity.
A basilar artery branch that supplies the anterior portion of the inferior surface of the cerebellum.
A organ cavity that is part of a pharyngotympanic tube.
Check relationships for conformance with AAO and XAO
A epithelium that is part of a hypopharynx.
A epithelium that is part of a vermiform appendix.
Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.
Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.
The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate.
requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip
An anatomical cavity that surrounded_by a stomodeum.
Epithelial sense organ containing the cupula housing a gelatinous material elongated from the basement of the organ toward the atrial cavity. The basement of the cupular organ consists of two cell types: sensory cells and support cell
possible homologues of neuromasts in the inner ear (Bone & Ryan, 1978; Wada et al 1998). In the tunicate cupular organ, the sensory cell is a primary neuron sending an axon to the CNS. The sensory cilium is within a deep indentation of the cell and is surrounded by a collar of short microvilli.
Mechanoreceptor organ found in oral siphon of botryllid ascidians, made of hair cells, similar to the vertebrate octavolateralis system. A possible candidate of the vertebrate lateral line.
Embryonic duct that is the rudiment of cerebral ganglion and and neural gland of adult in the ascidians.
Homology: candidate homolog for both neural crest and for the combined olfactory and adenohypophyseal placodes (Burighel et al., 2003; Manni et al., 2004a). Development: During formation of the adult ascidian, the ectodermal neurohypophyseal duct fuses with an evagination of the pharynx to form the neural gland rudiment
tubular appendage for drawing or ejecting fluids
One of sublaminar layers S1, S2, S3, or S4.
The region extending out from the boundary between layers S1 and S2.
The region extending out from the boundary between sublaminar layers S3 and S4.
A region of the retina corresponding to a portion of two adjacent substratum layers.
Was made obsolete as it was xenopus specific
The cavity of the developing embryo that is formed within the epiblast tissue prior to the closing of the proamniotic canal by the amniotic folds
The closed space containing the yolk, formed by the fusion of the edges of the embryonic epiblast (hypoblast) and later surrounded by the visceral yolk sac (hypoblast and visceral yolk sac mesoderm)
The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels
Lymph flows into the medullary sinuses from cortical sinuses, and into efferent lymphatic vessels. Medullary sinuses contain histiocytes (immobile macrophages) and reticular cells.[WP]
The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node
The crescent-shaped, ventrally located fold of the embryonic disc at the future cephalic end of the developing embryo
The crescent-shaped, ventrally located fold of the embryonic disc at the future caudal end of the developing embryo
The elevated margins of the neural groove that are located in the future cephalic region of the embryo
The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas
A thick layer of vascularized adipose tissue found under the skin of all cetaceans, pinnipeds and sirenians.
Lipid-rich, collagen fiber–laced blubber comprises the hypodermis and covers the whole body, except for parts of the appendages, strongly attached to the musculature and skeleton by highly organized, fan-shaped networks of tendons and ligaments. It can comprise up to 50% of the body mass of some marine mammals during some points in their lives, and can range from two inches (5 cm) thick in dolphins and smaller whales, to more than 12 inches (30 cm)thick in some bigger whales, such as right and bowhead whales
wax present in the head cavities of the sperm whale.
A biliary secretion of the intestines of the sperm whale.
A ganglion that is part of a abdominal segment of trunk.
An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx.
An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx.
the left duct atrophies at metamorphosis in the lamprey (22)[PMID:20959416, S1]
A anterior cardinal vein that is in_the_left_side_of a multicellular organism.
A anterior cardinal vein that is in_the_right_side_of a multicellular organism.
A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.
this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules
obsolete embryonic midbrain hindbrain boundary
A nuclear complex of the medullary reticular formation that can be divided into three subnuclei: the parvocellular, magnocellular and the subtrigeminal[WP,modified].
lateral group of medullary reticular formation
lateral reticular formation of the medulla oblongata
The lateral reticular nucleus, of the funiculus, can be divided into three subnuclei, the parvocellular, magnocellular and the subtrigeminal. As is typical of the reticular formation, none of these are very distinct subnuclei, but rather blurred distinctions between cell types and location. The lateral reticular nucleus sends all of its projections to the cerebellum. The parvocellular portion of the LRN and the immediately adjacent magnocellular portion send most their projections to the vermis of the cerebellum. The rest of the magnocellular subnucleus sends its projections to the hemisphere regions of the cerebellum. The subtrigeminal nucleus sends its projections to the flocculonodular lobe. All of these efferent pathways are projected in an ipsilateral manner to the cerebellum, the most abundant of which are those to the vermis. This nucleus is also involved in the mediation of inspiration (in-breathing) with a part of the ventral r. nucleus. The afferent pathways to the LRN come from the spinal cord and higher brain structures. Most of the afferents come from the ipsilateral dorsal horn of the spinal cord and project exclusively to the parts of the LRN that do not receive input from the cortex. The spinal cord projections terminate mostly in the parvocellular region along with the adjacent magnocellular cells. This implies that most input from the spinal cord is relayed into the vermis[WP]
A nucleus of brain that is part of a intermediate reticular formation.
Serous sac, which has as parts the pleura and the pleural cavity. Examples: There are only two canonical instances, right and left pleural sacs.
A cardiac muscle tissue that is part of a right atrium auricular region.
cardiac muscle of right auricular region
right atrium auricular region heart muscle
A cardiac muscle tissue that is part of a left atrium auricular region.
left atrium auricular region heart muscle
The dorsolateral prefrontal cortex (DL-PFC or DLPFC), according to a more restricted definition, is roughly equivalent to Brodmann areas 9 and 46.[1] According to a broader definition DL-PFC consists of the lateral portions of Brodmann areas 9 – 12, of areas 45, 46, and the superior part of area 47.[2] These regions mainly receive their blood supply from the middle cerebral artery. With respect to neurotransmitter systems, there is evidence that dopamine plays a particularly important role in DL-PFC.[2]DL-PFC is connected to the orbitofrontal cortex, and to a variety of brain areas, which include the thalamus, parts of the basal ganglia (the dorsal caudate nucleus), the hippocampus, and primary and secondary association areas of neocortex, including posterior temporal, parietal, and occipital areas
The frontal part of the cingulate cortex that resembles a collar form around the corpus callosum. It includes both the ventral and dorsal areas of the cingulate cortex. http://en.wikipedia.org/wiki/File:Gray727.svg
Posterior portion of the rhombic lip contained within rhombomeres 2-8. Gives rise to several brainstem nuclei and choroid plexus.
Anterior-most region of dorsal hindbrain within rhombomere 1, adjacent the midbrain-hindbrain boundary.
An acinus refers to any cluster of cells that resembles a many-lobed 'berry,' such as a raspberry (acinus is Latin for berry). The berry-shaped termination of an exocrine gland, where the secretion is produced is acinar in form, as is the alveolar sac containing multiple alveoli in the lungs.
Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204]
An anatomical space that surrounded_by a primitive urogenital sinus.
Mesenchyme that surrounds primitive urogenital sinus.
Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth
An epithelium that is part of a embryonic cloaca.
A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop.
A narrow stripe of cells that lies between the prospective dorsal and ventral thalami. This boundary contains signals that pattern the prethalamic and thalamic territories of the future mid-diencephalon.
Modeling this as a line may not be correct - see http://code.google.com/p/caro2/issues/detail?id=17
The border between the dorsal and ventral thalamus.[TAO]
wholly aquatic larval stage in the life cycle of an amphibian, particularly of a frog or toad[WP]. XAO: The stages from feeding to the end of metamorphosis. Encompasses Weisz's first-form tadpole (equivalent to NF stages 45 to 49), second-form tadpole (NF 49 to 56) and third-form tadpole (NF 56 to 60-plus) stages.
A multicellular organism that existence_starts_and_ends_during a nematode larval stage.
The intersection of sublaminar layers S4 and S5.
The intersection of sublaminar layers S2 and S3.
The part of the uterus above the isthmus and below the orifices of the uterine tubes.
Branch or outpocketing of the digestive tract.
non-contractile pouch that is connected to the anterior stomach through a slit-like opening. This pouch is also well-connected to the haemal system through numerous haemal ducts within its connective tissue layer.
The digestive tract of many metazoan invertebrates is characterized by the presence of caeca or diverticula that serve secretory and/or absorptive functions. With the development of various feeding habits, distinctive digestive organs may be present in certain taxa. This also holds true for sea urchins (Echinodermata: Echinoidea), in which a highly specialized gastric caecum can be found in members of a derived subgroup, the Irregularia (cake urchins, sea biscuits, sand dollars, heart urchins, and related forms)... Homologous with the more or less pronounced dilation of the anterior stomach that is observed in most "regular" sea urchin taxa[PMID:20955602]
A space enclosed within the laminae of the septum pelludicum, the membranous partition that seperates the frontal horns of the ventricle. contains cerebrospinal fluid (CSF) that filters from the ventricles through the septal laminae. bounded anteriorly by the genu of the corpus callosum; superiorly by the body of the corpus callosum; posteriorly by the anterior limb and pillars of the fornix; inferiorly by the anterior commissure and the rostrum of the corpus callosum; and laterally by the leaflets of the septum pellucidum.
In humans, present in 100% of fetuses, but over 85% of them fuse by 3–6 months after birth
A thin layer of connective tissue that lines the surface of the bony tissue that forms the medullary cavity of long bones
the CG appears to be a diencephalic brain. It originates mainly from the posterior sensory vesicle (Takamura 2002; Dufour et al. 2006) and shows endocrine activity. For examples, ascidian genes orthologous to GnRH and OT/VP, which are secreted from the hypothalamus and the NH, respectively, in vertebrates, are expressed in the cortex of the CG, suggesting that the NC is not distinctly compartmentalized as are vertebrate brains (Tsutsui et al. 1998; Kavanaugh et al. 2005; Kawada et al. 2008; Ukena et al. 2008; Kawada et al. 2009). Moreover, PC2 expression in the cortex of the CG supports possible endocrine activity (Sekiguchi et al. 2007). // Editor notes: consider merging into brain, based on http://www.ncbi.nlm.nih.gov/pubmed/21062451 "We suggest using the term ➞brain not only for the 'dorsal ganglia' of adult Tunicata and Pterobranchia, but also for the larval 'cerebral ganglion' of tunicates."
assumed to be a pituitary homolog. Current data from the Ciona genome suggests that the ascidian NC, including the CF, is unlikely to be a pituitary-like endocrine gland, while it is necessary to examine other ascidians before drawing a final conclusion [PMID:21558186]
A deep ciliated fossa on the dorsal midline of the buccal cavity (the region of the gut behind the mouth). Among other things, it secrets mucus which entraps food particles from the water[WP].
An unpaired kidney whose duct opens into the anterior pharynx. It can be seen as a deep ciliated fossa on the dorsal midline of the buccal cavity (mouth). Among other things, it secrets mucus which entraps food particles from the water[WP].
A Hatschek's diverticulum that is in the left side of a multicellular organism.
A Hatschek's diverticulum that is in the right side of a multicellular organism.
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach
outer portion of the renal cortex. Site of formation of medullary and cortical elements.
see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish.
Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton
Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad].
Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO]
The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]
Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present
we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad].
Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO]
Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad].
The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone
we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
One of a number of vertical folds, produced by an infolding of the mucous membrane and some of the muscular tissue in the upper half of the lumen of the anal canal. They are named after Giovanni Battista Morgagni who also has several other eponyms named after himself[WP]
A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla.
Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla
One of a set of curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries.
The interlobar veins are veins of the renal circulation which drain the renal lobes.
A local thickening of cells that acts as a margin separating sheets of cells from posterior margin of avian blastoderms from hypoblasts as they migrate anteriorly to push primary hypoblast cells anteriorly to form a secondary hypoblast known as the endoblast
A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract).
extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708].
In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11–14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested
in mouse has left ventricular identity[PMID:22855565]
Mesenchyme that is part of a developing face.
An auditory cortex that is in the left side of a brain.
An auditory cortex that is in the right side of a brain.
The anterior end of the hemisphere is named the frontal pole. The posterior end is named the occipital pole. The anterior end of the temporal lobe, the temporal pole.
A nerve root that extends_fibers_into a nerve connecting eye with brain.
TODO - check. See comments for optic tract. FMA also has medial root.
todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)
The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP].
human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys
The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys
Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis
An anatomical wall that is part of a ureter.
The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary
The loose collection of neurons that reside in the rostral medulla close to the medullary surface, ventral and immediately caudal of nVII, that are crucial for CO2 sensing in the brain
The smooth muscle tissue surrounding the epithelium of the ureter
humeral diverticulum of clavicular air sac
check if the NIF class is actually a grouping class
The main olfactory bulb has a multi-layered cellular architecture. In order from surface to the center the layers are: Glomerular layer, External plexiform layer, Mitral cell layer, Internal plexiform layer, Granule cell layer[WP].
the structure in many ontologies called simply 'olfactory bulb' may in fact belong here
A narrow layer of cells located between the granule cell layer and hilus of the dentate gyrus, where adult neurogenesis occurs.
A multicellular organism that existence_starts_with a post-embryonic stage.
A vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants
check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]
Cranial placode with neurogenic potential[cjm]. Neurogenic placodes are transient ectodermal thickenings that form at the border of the neural plate and epidermis and give rise to sensory neurons of the cranial ganglia[ZFA]. The neurogenic placodes give rise to parts of various nerves and ganglia, the olfactory organ, parietal eye, parts of the inner ear, and the lateral line. There are 2 major series of neurogenic placodes, the dorsolateral and ventrolateral or epibranchial[PMID]
Includes: trigeminal, otic, lateral line and epibranchial placodes.
While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)
A specialised sensory organ located in the subepidermal connective tissue at the rostral end of late larval and adult amphioxus. They consist of between 1 and 4 nerve cells with axons, each with 2 cilia, surrounded by up to 7 sheath cells. The cilia extend into a protrusion of the basal lamina which surrounds each corpuscle. The axonal process contributes to the rostral nerve.
Development: joins with Hatschek’s diverticulum to form Hatschek’s pit in the adult. Location: anterior to the mouth.
A anatomical space that is enclosed by a urinary bladder.
A anatomical space that is enclosed by a oropharynx.
A circular muscle layer of muscular coat that is part of a esophagus.
inner circular muscle layer of esophagus
outer longitudinal muscle layer of esophagus
esophagus smooth muscle longitudinal layer
A gland that discharges its secretion through a duct opening on an internal or external surface of the body, as a lacrimal gland.
Excretory gland situated in the basal article of the antennal peduncle. It functions to rehulate ionic balance
consider also classifying this as a renal tubule - or separate terms for coiled/nephridial canal
Excretory organ in maxillary segment with duct opening on maxilla.
consider generalizing to include millipedes, centipedes. Function: Two different excretory organs are found among crustaceans: the antennal gland and the maxillary gland. Both have the same basic structure: an end sac and a convoluted duct that may expand into a bladder before opening to the outside. In most adult crustaceans only one or the other gland functions. The functional gland may change during the life cycle. Terminology note: http://crustacea.nhm.org/glossary/define.html?termID=327 suggests green gland as the generic term and antennal as the decapoda term
A gland found in some arthropods, for collecting and excreting urine. The gland comprises an end sac (saccule), a long duct (labyrinth) and a terminal bladder (reservoir). There is generally only one pair (two in some spiders), and they open on the coxae of the walking legs[WP].
They are found in all arachnids (with the exception of some Acari), and in other chelicerates, such as horseshoe crabs. Homology: The coxal gland is thought to be homologous with the antennal gland of crustaceans
Subdivision of conducting system of heart which consists of the anterior, middle and posterior internodal tracts beneath the endocardium of interatrial septum and above the attachment of the septal leaflet of tricuspid valve.
evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial
An epithelium that is part of a pancreatic duct.
in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this
one of the gastric glands that secretes the hydrochloric acid of the gastric juice[Stedman's].
FMA has this as part of both the fundus and the body, but these are largely spatially disjoint.
The junction between the ureter and the renal pelvis of the kidney
The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney
An anatomical cavity that surrounded_by a Rathke's pouch.
An intrinsic circulatory network that transports hormones from the median eminence of the hypothalamus to the adenohypophysis.
we represent this structure strictly as a system of blood vessels (presumably in line with the FMA). It could also be extended to include neurons and fiber tracts, as per the MESH definition
in lampreys and teleost hormones enter the adenohypophysis by diffusion. .
One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis). The hypothalamus is responsible for certain metabolic processes and other activities of the autonomic nervous system. It synthesizes and secretes certain neurohormones, often called hypothalamic-releasing hormones, and these in turn stimulate or inhibit the secretion of pituitary hormones. The hypothalamus controls body temperature, hunger, thirst, fatigue, sleep, and circadian cycles
Predeciduous teeth present at birth. They may be well formed and normal or may represent hornified epithelial structures without roots. They are found on the gingivae over the crest of the ridge and arise from accessory buds of the dental lamina ahead of the deciduous buds or from buds of the accessory dental lamina. (From Jablonski, Dictionary of Dentistry, 1992)
grouping class that collected the entepicondyles and epicondyles icondyles of humerus and femur
An articular prominence of a bone, typically present in pairs, resembling a pair of knuckles. Examples: Condyle of humerus, condyle of femur.
Protuberance on a bone that participates in a joint with another bone.[TAO]
the round prominence at the end of a bone, most often part of a joint - an articulation with another bone[WP][Wikipedia:Condyle_(anatomy)].
A condyle that is part of a distal epiphysis of femur.
Convex articular facet of the distal head of the femur that articulates with the proximal head of the fibula.[AAO]
The medial condyle is one of the two projections on the lower extremity of femur. The medial condyle is larger than the lateral (outer) condyle due to more weight bearing caused by the center of gravity being medial to the knee. On the posterior surface of the condyle the linea aspera (a ridge running down the posterior shaft of the femur) turns into the medial supracondylar ridge. The outermost protrusion on the medial surface of the medial condyle is referred to as the 'medial epicondyle' and can be palpated by running fingers medially from the patella with the knee in flexion.
The lateral condyle is one of the two projections on the lower extremity of femur. It is the more prominent and is the broader both in its antero-posterior and transverse diameters
The lateral epicondyle of the femur, smaller and less prominent than the medial epicondyle, gives attachment to the fibular collateral ligament of the knee-joint. Directly below it is a small depression from which a smooth well-marked groove curves obliquely upward and backward to the posterior extremity of the condyle.
The medial epicondyle of the femur is a bony protrusion located on the medial side of the bone's distal end. Located above the medial condyle, it bears an elevation, the adductor tubercle, which serves for the attachment of the superficial part, or 'tendinous insertion', of the adductor magnus. This tendinous part here forms an intermuscular septum which forms the medial separation between the thigh's flexors and extensors. Behind it, and proximally to the medial condyle is a rough impression which gives origin to the medial head of the Gastrocnemius.
The distal end of the humerus, including the trochlea, capitulum and the olecranon, coronoid and radial fossae
As in the N.A., the Condylus humeri is the whole distal end of the bone except the epicondyles. The Capitulum humeri is present in Carnivora, more distinctly in the cat than in the dog. The Fossa coronoidea, present in the cat is medial to the Fossa radialis and accommodates the Processus coronoideus medialis ulnae when the elbow is flexed. A Foramen supratrochleare occurs in carnivora and occasionally in pig.[NOMINA ANATOMICA VETERINARIA (2005)]
One of the lateral or medial condyles of the tibia.
Convex articular facet of the distal head of the femur that articulates with the proximal head of the tibia.[AAO]
The medial condyle is the medial portion of the upper extremity of tibia. It is the site of insertion for the Semimembranosus muscle[WP].
The lateral condyle is the lateral portion of the upper extremity of tibia. It serves as the insertion for the Biceps femoris muscle[WP].
The ganglion found on the root of each cranial nerve, containing the cell bodies of afferent (sensory) neurons.
A chorionic villus that is a solid outgrowth of the cytotrophoblast that protrudes into the syncytiotrophoblast.
A chorionic villus that is has a core of loose connective tissue, which in humans grows into the primary villi about the third week of development.
Tertiary chorionic villi contain embryonic blood vessels that develop from mesenchymal cells in the loose connective tissue core. These blood vessels connect up with vessels that develop in the chorion and connecting stalk and begin to circulate embryonic blood about the third week of development in humans.
An anatomical structure that has more than one cell as a part.
A multicellular anatomical strucure consisting of a few cells of various types which forms a discrete structure with a largely bona fide boundary.
corpuscular, organoid structures composed of PNECs, found as distinctive innervated clusters only within intrapulmonary airways, where they appear concentrated at airway branch points; NEBs reach from the basement membrane to the airway lumen and are thought to function as oxygen sensors.
The vascularized and branched structures arising from the rodent trophoblast-derived epithelium that allow an increase its surface area for the efficient exchange of nutrients and wastes between the maternal and fetal circulation
The spaces of the placenta occupied by maternal blood, into which the fetal labyrinth villi project
The spaces of the placenta occupied by fetal blood, primarily within the fetal labyrinth villi
Round structure consisting of chorionic villi[PMID]. A separation of the decidua basalis of the placenta, separated by placental septa. Each cotyledon consists of a main stem of a chorionic villus as well as its branches and subbranches. The cotyledons receive fetal blood from chorionic vessels, which branch off cotyledon vessels into the cotyledons, which, in turn, branch into capillaries. The cotyledons are surrounded by maternal blood, which can exchange oxygen and nutrients with the fetal blood in the capillaries[WP].
Rodents have a single cotyledon (called a discoid placenta), whereas humans have multiple cotyledons, although they are consolidated into a cluster that resembles a single disc[PMID:19829370]
A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF].
May be obsoleted. The FMA class is more specific
A group of neurons in the basal forebrain that has wide projections to the neocortex and is rich in acetylcholine and choline acetyltransferase. It undergoes degeneration in paralysis agitans and Alzheimer's disease.
rich in acetylcholine and choline acetyltransferase
The NBM is inferior to the globus pallidus and within an area known as the substantia innominata
basal magnocellular nucleus (substantia innominata)
nucleus of the horizontal limb of the diagonal band (Price-Powell)
Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum.
it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
An elongate paired tissue ventral to the kidneys and partialy enveloping the anterior gonads in Elasmobranchii. Apparently important to the immune system
The ventralmost of the two bodies of the elasmopbranch hemopoietic organ betweean the esophageal mucosa and muscularis
Gradation varies in species. In the stingray, two distinct lobes are seen, in the banded dogfish each lobe is divided into lobules [Homma et al 1984]
Coiled structure in the lumen of the small intestine that increases the length of the route through the diesgtive tract.[WP,cjm,Kardong]
A series of crescentic folds of mucous membrane somewhat spirally arranged on the interior of the gallbladder and continuing into the cystic duct
The spiral valve alternately blocks & unblocks the entrances to the left and right pulmonary arches (sending unoxygenated blood to the skin & lungs).
The spiral valve is considered to have evolved from the right member of the four embryonic endocardial ridges (Goodrich, 1930 - via Morris 1974)
A small hole behind each eye that opens to the mouth in some fish. In the primitive jawless fish the first gill opening immediately behind the mouth is essentially similar to the other gill openings.
In elasmobranchs (sharks and rays), a spiracle is found behind each eye, and is often used to pump water through the gills while the animal is at rest (Fouts, 2003). A spiracle is also found in primitive bony fishes as the chirrups.
The spiracle is still found in all cartilaginous fish except chimaeras, and in bony fishes in the coelacanth, sturgeon, paddlefish and bichirs. It is also seen as an otic notch in the skull of the extinct labyrinthodonts, and is thought to be associated with the ear opening in amniotes and frogs
GO term spiracle morphogenesis, open tracheal system - does not refer to this structure
The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity.
The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG]
in humans, dorsal diverticulum deepens as the tubotympanic recess to form the auditory tube
dorsal elongation of first pouch endoderm
in humans, the ventral portion of pouches 1 and 2 are obliterated by the developing tongue
ventral elongation of first pouch endoderm
in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN10:1607950324]. the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract
dorsal elongation of second pouch endoderm
ventral elongation of second pouch endoderm
Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III)
dorsal 3rd arch pharyngeal pouch endoderm
cranial dorsal aspect of third dorsal pharyngeal pouch
The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium
ventral 3rd arch pharyngeal pouch endoderm
caudal ventral aspect of third dorsal pharyngeal pouch
Mesenchyme that is part of a pharyngeal arch 6.
The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch.
The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue
The Posterior tongue, or pharyngeal part, is the part of the tongue behind the terminal sulcus. At its root, it is directed backward, and connected with the hyoid bone by the Hyoglossi and Genioglossi muscles and the hyoglossal membrane; with the epiglottis by three folds (glossoepiglottic) of mucous membrane; with the soft palate by the glossopalatine arches; and with the pharynx by the Constrictores pharyngis superiores and the mucous membrane. It is derived primarily from the third pharyngeal arch. (The second arch has a substantial contribution during fetal development, but this later atrophies. The fourth arch may also contribute, depending upon how the boundaries of the tongue are defined.)
A single midventral prominence deriving from the ventral bases of pharyngeal arches 2, 3 and 4 - provides the covering of the posterior of the tongue //The furcula is at first separated from the tuberculum impar by a depression, but later by a ridge, the copula, formed by the forward growth and fusion of the ventral ends of the second, third, and part of the fourth branchial arches[WP].
add new term for Hypobranchial_eminence?
A group of cells located ventral to the decussation of the superior cerebellar peduncle in the mouse ( Paxinos-2001 ) and rat ( Swanson-1998 )
The fundus glands (or fundic glands, or gastric glands) are found in the body and fundus of the stomach. They are simple tubes, two or more of which open into a single duct.
Consider FMA:14923 ! Principal gland of fundus of stomach. Added part_of to mucosa to be consistent with FMA pattern (note that Kardong places this in the glandular epithelium)
An organ of the digestive tract that is capable of retaining and storing food
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
Am epithelium that lines the stomach which lacks glands. In addition to a glandular epithelium, the stomachs of some vertebrates also has a second region characterized by a nonglandular epithelium, devoid of gastric glands.
todo - clarify if mucus glands are also excluded, in addition to gastric glands. See notes for rumen.
this region may develop from the base of the esophagus (some herbivores) - in rodents, loss of the gastric glands in the mucosa leavea a nonglandular epithelial stomach in which smooth muscle contractions knead and mix digesta. This can be keratinized.
In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
Mesenchyme that is part of a pharyngeal arch 1.
Mesenchyme that is part of a 1st arch maxillary component.
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
entire pharyngeal arch associated mesenchyme
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
A gland situated on the upper lip found in non-venomous snakes. Releases secretion via duct adjacent to posterior maxillary teeth.
Glandular tissue present in lips of reptiles.
The dosralmost of the two bodies of the elasmopbranch hemopoietic organ betweean the esophageal mucosa and muscularis
A mucosa that is part of a dorsum of tongue.
develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN10:1607950324
A malleus endochondral element that is composed primarily of a cartilage tissue.
A stapes endochondral element that is composed primarily of a cartilage tissue.
The stapes is homologous to the hyomandibula. In this ontology, we use the class 'hyomandibular cartilage' generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks.
A compound organ that has_potential_to_develop_into a tongue.
On the lateral wall of the nasal part of the pharynx is the pharyngeal opening of auditory tube (pharyngeal ostium), somewhat triangular in shape, and bounded behind by a firm prominence, the torus or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane.
pharyngeal orifice of pharyngotympanic tube
pharyngeal ostium of pharyngotympanic tube
pharyngeal opening of pharyngotympanic tube
An anatomical space with at least one opening to another space or the exterior.
The tympanic part of the temporal bone is a curved plate of bone lying below the squama and in front of the mastoid process.
TODO distinguish ecto- and ento- tympanics
consider merging with tympanic ring. See discussion page on wikipedia page for ectotympanic
A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane
outer cuticular layer of tympanic membrane
tympanic membrane external acoustic meatus epithelial component
outer epithelial layer of tympanic membrane
The intermediate fibrous layer of the tympanic membrane.
connective tissue layer of tympanic membrane
intermediate fibrous layer of tympanic membrane
In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer
The cells of the body which stain with chromium salts. They occur along the sympathetic nerves, in the adrenal gland, and in various other organs.
in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies
One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia.
Tissue cavity consisting of intercommunicating trabecular spaces in the cancellous bone.
network of trabecular spaces in bone tissue
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
Consider merging with capillary layer. Consider choriocapillaris complex
A plexus of capillaries that is located anteromedial to the eye. It is a capillary layer in the choroid. It is in contact with the basal surface of the retinal pigmented epithelium and supplies the photoreceptors with oxygen and nutrients. The fused basement membrane of this capillary layer and the pigmented epithelium is called Bruch's membrane.[XAO:0004176].
Is an ocular vasculature that develops adjacent to the pigment epithelium of the eye. The optic choroid vascular plexus develops from the primitive mesencephalic artery. Initially blood enters from the mesencephalic central artery, and the dorsal ciliary vein. The plexus drains via the ophthalmic vein. The plexus supplies blood to the retina[ZFA:0005094].
The choroid of teleosts is a connective tissue layer rich in blood vessels, and one or two choroidal glands.
An extrahepatic bile duct that has_potential_to_develop_into a common hepatic duct.
Mesenchyme that has_potential_to_develop_into a dermis.
A multi-tissue structure that has_potential_to_develop_into a diaphragm.
A developing anatomical structure that has_potential_to_develop_into a falx cerebri.
A multi-tissue structure that has_potential_to_develop_into a meninx of hindbrain.
A developing anatomical structure that has_potential_to_develop_into a metencephalon.
A developing anatomical structure that has_potential_to_develop_into a myelencephalon.
A gray matter that has_potential_to_develop_into a facial nucleus.
A gray matter that has_potential_to_develop_into a inferior salivatory nucleus.
A gray matter that has_potential_to_develop_into a superior salivatory nucleus.
A gray matter that has_potential_to_develop_into a nucleus ambiguus.
A gray matter that has_potential_to_develop_into a dorsal motor nucleus of vagus nerve.
A ganglion that has_potential_to_develop_into a pterygopalatine ganglion.
future sphenopalatine parasympathetic ganglion
A femur endochondral element that is composed primarily of a cartilage tissue.
The distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw)
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
A small blood vessel in the abdomen that supplies blood directly to the pylorus (distal part of the stomach) and proximal part of the duodenum, and indirectly to the pancreatic head (via the anterior and posterior superior pancreaticoduodenal arteries).
any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli
A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid.
A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid.
An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
A sex cord that is part of a indifferent gonad.
note that this represents the indifferent structure.
A bodily secretion that secreted_by a seminal vesicle.
in ncit, seminal fluid is a subtype of seminal vesicle secretion
the numerous mucous-secreting glands found in several female mammalian species (including rodents and humans) on the anterior wall of the vagina, around the lower end of the urethra, and possessing a common paraurethral duct which opens (on each side) near the external urethral orifice; they are homologous with the prostate gland in males, have highly variable anatomy, and are believed to be the source of the female ejaculate, a lubricating fluid with a similar consistency to male prostatic fluid that is expelled through the urethra during sexual stimulation; like the male prostate, these glands are susceptible to infection (skenitis), cyst development, and cancer
in MP female urethral gland, Skene gland and paraurethral gland are exact syns. Note that NCITA seems to use the term in a more generic way, as a parent for skene gland, cowper gland (which may be the same as the male bulbo-urethral gland)
The Skene's ducts are a pair of ducts leading from the Skene's glands to the surface of the vulva, to the left and right of the urethral opening.
FMA has separate class 'duct of paraurethral gland' (FMA:21860)
ductus paraurethrales urethrae femininae
Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
A gelatinous secretion used in the mating of some species. It is deposited by a male into a female genital tract and later hardens into a plug or glues the tract together.
One of a pair of ducts leading from the Bartholin's glands to the surface of the vulva
A duct that is part of a bulbo-urethral gland.
A mucous secretion that is produced by glands in the epidermis.
The inner mucosa of the fourth stomach chamber of a ruminant produces rennet.
unites the mastoid process of the temporal with the region of the mastoid angle of the parietal[WP:Squamosal_suture].
The Sphenofrontal suture is the cranial suture between the sphenoid bone and the frontal bone.
The Sphenoparietal suture is the cranial suture between the sphenoid bone and the parietal bone.
The Sphenozygomatic suture is the cranial suture between the sphenoid bone and the zygomatic bone.
The occipitomastoid suture is the cranial suture between the occipital bone and the mastoid portion of the temporal bone. It is continuous with the lambdoidal suture.
An anatomical cavity that surrounded_by a lymphatic vessel.
An anatomical cavity that surrounded_by a blood vessel.
The eyebrow is an area of thick, delicate hairs above the eye that follows the shape of the lower margin of the brow ridges. Their main function is to protect the eye, but they are also important to human communication and facial expression. It is not uncommon for people to modify their eyebrows by means of hair addition or removal, make up, or piercings.
An anatomical cluster that composed_primarily_of a strand of hair.
A collection of hairs that is part of a face.
The collection of hair that grows on the chin, cheeks and neck of human beings. Usually, only pubescent or adult males are able to grow beards. However, women with hirsutism may develop a beard. When differentiating between upper and lower facial hair, a beard specifically includes the moustache, which refers to hair above the upper lip and around it.
A collection of hair on face that is part of a eyelash.
facial hair grown on the outer surface of the upper lip. It may or may not be accompanied by a type of beard, a facial hair style grown and cropped to cover most of the lower half of the face.
A strand of hair that is part of a face.
The portion of the left ventricular outflow tract delineated by the sinotubular ridge superiorly and the bases of the valve leaflets inferiorly; it comprises the aortic sinuses, the aortic valve leaflets, the commissures, and the interleaflet triangles
The dilated first part of the aorta containing the aortic semilunar valves and the aortic sinuses.
The point in the ascending aorta where the aortic sinuses end and the aorta becomes a tubular structure
A phagocytic sleeve that is part of a sheathed arteriole of the spleen, and is sometimes referred to as a splenic ellipsoid. It is a spindle-shaped thickening in the walls of the second part of the arterial branches forming the penicilli in the spleen
A vein or veins draining a bone and emerging from a nutrient foramen.
The medullary or nutrient artery, usually accompanied by one or two veins, sends branches upward and downward to the bone marrow, which ramify in the medullary membrane, and give twigs to the adjoining canals.
The straight venules of kidney are branches from the plexuses at the apices of the medullary pyramids, formed by the terminations of the arteriae rectae. They run outward in a straight course between the tubes of the medullary substance, and joining, as above stated, the interlobular veins, form venous arcades; these in turn unite and form veins which pass along the sides of the pyramids. Contains fenestrated capillaries.
A structure formed from the primary sex cords in females, counterpart of the rete testis in males.
any of the numerous small mucous-secreting glands located in the wall of the penile urethra
glandulae urethrales urethrae masculinae
An urethral gland that is part of a female urethra.
the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation
One of the laterally paired arteries that supply the gonads.
A portal vein that empties into capillaries within the kidneys.
A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver.
Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO]
A portal system that transports blood returning from capillary beds within tail or hindlimbs through paired renal portal veins that empty into capillaries within the kidneys.
Part of the circulatory system in which the veins of the hindlimb combine to form the pair Jacobson's veins which receive many small vesicles from the kidney and also collects blood from the oviducal vein.[AAO]
present in all classes of vertebrates except mammals; the mammalian kidney has a low pressure vascular network that may be its counterpart
The initial part of the entire common carotid artery ending with the point where the artery bifurcates into an external carotid artery and an internal carotid artery.
A segment of the embryonic dorsal aorta between points of juncture with the third and fourth arch arteries; it regresses early in development to allow the carotid axis to take its definitive appearance.
An anatomical boundary that corresponds to some physical discontinuity.
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
The lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line develops from cranial ectodermal placodes situated behind the ear and between the eye and ear.
A vasculature that is part of a post-anal tail.
One of the several veins that drain the mesencephalon; the posterior ones are tributaries to the great cerebral vein; the lateral ones are tributaries to the basal vein. The main veins are: pontomesencephalic vein [TA] (vena pontomesencephalica [TA]), interpeduncular veins [TA] (venae interpedunculares [TA]), intercollicular vein [TA] (vena intercollicularis [TA]), and lateral mesencephalic vein [TA] (vena mesencephalica lateralis [TA])[MedLex]. The major vein of the midbrain, which crosses the midbrain medially to meet it's partner the mesencephalic artery[XAO].
review this term, check taxon scope; note FMA has specific subtypes
A fold of the mucous membrane of the conjunctiva in many animals. At rest, it is hidden in the medial canthus. It can extend to cover part or all of the cornea to help clean the cornea.
We exclude the shark structure for this via a taxon constraint.
in mice, the nictitating membrane is very small and composed of a very thin core of cartilage covered by loose connective tissue
Some reptiles, birds, and sharks have full nictitating membranes; in many mammals, a small, vestigial portion of the membrane remains in the corner of the eye. Some mammals, such as camels, polar bears, seals, and aardvarks, have full nictitating membranes. fully developed nictitating membranes can be found in lemurs and lorisoid primates.
The plica semilunaris is a small fold of bulbar conjunctiva on the medial canthus of the eye. It is loose, so that eye movements are not restricted. It is considered a vestigial organ.
A semisolid gelatinous mass of coagulated blood that consists of red blood cells, white blood cells, and platelets entrapped in a fibrin network.
Highly vascularized tissue that replaces the initial fibrin clot in a wound. Vascularization is by ingrowth of capillary endothelium from the surrounding vasculature. The tissue is also rich in fibroblasts (that will eventually produce the fibrous tissue) and leucocytes.
Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring.
check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton
paired primordial elevations, on either side of the embryonic larynx, within which the arytenoid cartilages are formed
EHDAA2 and EMAPA appear to be inconsistent
arytenoid swelling pre-cartilage condensation
Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6?
A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified].
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
A portion of organism substance that is produced a rumen.
A muscular structure at the lower end of the esophagus that, when closed, forms a tube allowing milk to go directly into the abomasum. (This prevents milk from being fermented or soured by the ruminal microorganisms).
The formation of the esophageal groove is controlled by neural stimulation from suckling and milk proteins. This means milk, colostrum, and milk replacer bypass the rumen, while water enters it
The camera-type eye apart from its appendages/adnexa.
The connective tissue that supports the lobules and follicles of the thyroid gland.
The palatopharyngeus or palatopharyngeal or pharyngopalatinus muscle is a long, fleshy fasciculus, narrower in the middle than at either end, forming, with the mucous membrane covering its surface, the palatopharyngeal arch.
Palatopharyngeus is a muscle that attaches to the palatine bones, soft palate, and pharynx and is innervated by Cranial Nerve X via the pharyngeal plexus.[FEED]
It is separated from the palatoglossus muscle by an angular interval, in which the palatine tonsil is lodged. It arises from the soft palate, where it is divided into two fasciculi by the levator veli palatini and musculus uvulae
The musculus uvulae (azygos uvulae) is a muscle of the soft palate. It arises from the posterior nasal spine of the palatine bones and from the palatine aponeurosis. It descends to be inserted into the uvula and functions to move and shape it. It is innervated by the pharyngeal branch of the vagus nerve via the pharyngeal plexus[WP].
The muscle of the uvuli is an integral part of the soft palate and is innervated by Cranial Nerve X .[FEED]
A fleshy protuberance at the pylorus of some species such as ruminants and pigs, that projects into the lumen of the pyloric canal
A variant of the ascending colon in ruminants and pigs.
A salivary gland best developed in carnivores; located above the zygomatic arch and below the eye. Enlargement or mucocele of the gland causes exophthalmos
a variety of mammals have salivary glands variously terms upper molar/buccal gland - this class groups all of these
the racemose, mucous or serous glands in the submucous tissue of the cheeks
One in which the secretory cells maintain their integrity throughout the secretory cycle.
A tapetum lucidum that is part of the choroid. The choroidal tapetum lucidum lies immediately adjacent to the choriocapillaris and external to the retinal epithelium
we make the assumption that the BTO class belongs here rather than with the parent; the other type is the retinal type
A tapetum lucidum that is part of the retina, within the cytoplasm of the retinal epithelium
In crocodilians, a semicircular area of the retinal epithelium in the superior fundus shows a fair sulfur yellow coloration and is specialized as a tapetum lucidum.
In the tapetal area, no melanosomes are formed indicating a nonocclusible tapetum in the Caiman sclerops.
Retinal tapeta lucida are common in fish and some reptiles, but rarely occur in mammals. In most of these species the retinal tapetum can be classified as either a lipid (in some teleosts, mammals) or guanine type (in some teleosts, reptiles). Another differentiation can be made among the retinal tapeta lucida based on whether the tapetum is occlusible (found in most of teleosts), or nonocclusible (or static) (found in mammals)
as seen in teleosts, crocodiles, marsupials and fruit bats
the tapetum lucidum is an integral part of the pigment epithelium in primitive teleosts (lying in the pro- cesses of the pigmented epithelial cells). It can vary in chemical nature.
A choroid tapetum lucidum that is made of a palisade of cells containing stacks of flat hexagonal crystals of guanine
A choroidal tapetum of reflecting cells lying immediately outside the choriocapillaris is formed in a few primitive teleosts.
The elasmobranch tapetum in Squalus and Scyliorhinus con- sists of sheets of 12–13 superposed guanine crystals in the choroid.
elasmobranchii (skates, rays, and sharks) and chimaeras
A choroid tapetum lucidum that consists of layers of cells containing organized, highly refractive crystals. These crystals are diverse in shape and makeup
The choroidal stroma adjacent to the tapetum lucidum contains numerous small blood vessels that penetrate the tapetal layer to form a single-layered capillary network, known as the choriocapillaris, on the surface of the tapetum. The tapetum cellulosum is thus interposed between the large branching vessels in the choroid and the single layer of the choriocapillaris beneath the retinal epithelium[PMID:14738502]
A choroid tapetum lucidum that is an array of extracellular fibers.
The posterior meningeal artery are small vessels which are branches of the ascending pharyngeal artery which supply the dura mater. It passes through the mastoid foramen before entering the cranium via the jugular foramen.
terminal branch of ascending pharyngeal artery
meningeal branches of the ascending pharyngeal artery
The middle meningeal artery is typically the third branch of the first part (retromandibular part) of the maxillary artery; one of the two terminal branches of the external carotid artery. After branching off the maxillary artery in the infratemporal fossa, it runs through the foramen spinosum to supply the dura mater and the calvaria. The middle meningeal artery is the largest of the three (paired) arteries which supply the meninges, the others being the anterior meningeal artery and the posterior meningeal artery. In approximately half of subjects it branches into an accessory meningeal artery. The middle meningeal artery runs beneath the pterion. It is vulnerable to injury at this point, where the skull is thin. Rupture of the artery may give rise to an epidural hematoma.
A meningeal branch to the dura mater arising from the anterior ethmoidal artery.
this needs checking as part of a general revision of the blood vessels and their branches - unclear if the anterior meningeal artery should be treated separately from the anterior ethmoidal artery (ie as a branch) or the same thing
anterior meningeal branch of anterior ethmoidal artery
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme.
1st arch maxillary mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme.
pharyngeal arch 2 mesenchyme from neural crest
branchial arch 2 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme.
3rd pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 3rd arch
pharyngeal arch 3 mesenchyme from neural crest
branchial arch 3 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.
4th pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from neural crest
branchial arch 4 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
pharyngeal arch 6 mesenchyme from neural crest
branchial arch 6 mesenchyme from neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
mesenchyme derived from neural crest of mesenchyme of 1st arch
pharyngeal arch 1 mesenchyme from neural crest
branchial arch 1 mesenchyme from neural crest
One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton’s jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta.
The most posterior portion of the inferior frontal gyrus of the frontal lobe in the brain. In an axial plane, the Sylvian fissure extends from the operculum posteriorly to divide the frontal from the temporal lobe. Broca's area is a notable part of the operculum, which plays a key role in conversation or speech production, reading and writing. Its vascular supply comes from the M3 branches of the middle cerebral artery[WP].
Embryoid bodies are structures resembling embryos, occurring in several types of germ cell tumors.
Obsoled, as does not cover naturally occurring entity
An organ of the digestive tract of arthropods and molluscs. It provides the functions which in mammals are provided separately by the liver and pancreas, including the production of digestive enzymes, and absorption of digested food.
Digestive gland of crustaceans with functions approximately analogous to liver and pancreas of vertebrates - enzyme secretion, food absorption and storage.
Cranial nerve VI innervated; ventral and posterior to the eye.
In most other mammals it also innervates the musculus retractor bulbi, which can retract the eye for protection
A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage
Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO]
relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO]
In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process).
A zone of bone organ that is part of a hyoid bone.
An anatomical conduit that is part of a vertebra.
in AAO this is a space rather than conduit
The part of the embryonic mesentery which connects the embryonic heart with the body wall in front and the foregut behind.
There are two Pericardial sinuses: transverse and oblique. The cul-de-sac enclosed between the limbs of the inverted U of the venous mesocardium lies behind the left atrium and is known as the oblique sinus. . The passage between the venous and arterial mesocardiabi.e. , between the aorta and pulmonary artery in front and the superior vena cava behindbis termed the transverse sinus. Also, the sinus that forms in the pericardial cavity where the dorso-mesentary pericardium reside. Can be used to pass ligature during cardiac surgery.
The cul-de-sac enclosed between the limbs of the inverted U of the venous mesocardium lies behind the left atrium.[WP,unvetted].
A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi.
collect tears produced by the lacrimal glands
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
motor component of the VIIth (facial) nerve
Circular cartilage ringing the posterior portion of the eye in the sclera. Supports the eye.
consider distinguishing cup from predecessor of ossicle. Hall: The scleral cartilaginous cup is a distinctly sepa- rate element composed of hyaline cartilage
Bilaterally paired thin continuous band of cartilage that sagittally encircles the eye.[TAO]
May be calcified in chondrichthyans. Tetrapods without this element (e.g., snakes and mammals) have a collagenous sclera. May not be homologous - see http://www.ncbi.nlm.nih.gov/pubmed/17051547. cup-shaped in birds. Present in monotremes.
A bony plate around the eyes, are situated at the corneal-scleral limbus. They do not articulate with other elements of the skull. Typically, the scleral ossicles overlap the rim of a cup of scleral cartilage that supports the eyeball. Situated near the equator of the eye and may slightly overlap the rim of scleral cartilage.
The distribution of scleral ossicles and scleral cartilage among verte- brate taxa is not the same. Some taxa (e.g., birds) have both elements; some only have one element (e.g., crocodiles only have a scleral cartilage); while others (e.g., snakes) have neither element (Walls, 1942) number of ossicles making up the sclerotic ring as well as the shape of both the individual plates and the sclerotic ring is variable among tetrapod taxa.... It is therefore extremely likely that scleral skeletal elements (ossicles and cartilage) of all rep- tiles (including birds) are homologous (but cannot be assumed for reptiles and teleosts)
The function of these elements is to support the eye from within the sclera; scleral ossicles play an additional important role during accommodation in terrestrial vertebrates (Lemmrich, 1931; Walls, 1942; King and McLelland, 1984).
The episclera is the outermost layer of the sclera. It is composed of loose, fibrous, elastic tissue and attaches to Tenon's capsule. A vascular plexus is found between the conjunctiva and the sclera consisting of two layers of vessels, the superficial episcleral vessels and the deep episcleral vessels.
On the external surface of the sclera is a thin membrane, the suprachoroid lamina, composed of delicate non-vascular lamellaebeach lamella consisting of a net-work of fine elastic fibers among which are branched pigment cells. The spaces between the lamellC& are lined by endothelium, and open freely into the perichoroidal lymph space, which, in its turn, communicates with the periscleral space by the perforations in the sclera through which the vessels and nerves are transmitted.
An endothelium that is part of a sclera.
An eye adnexal structure, but not necessarily part of the eyeball
A pair of small dish-shaped bones that cap the anterior and posterior margin of the eyeball.[TAO]
The scleral ossicles [of teleosts] are reported to form indirectly by endochondral (Hall and Miyake, 1992) or by perichondral ossification (Patterson, 1977) from a cartilage element that is also present in the sclera. This is unlike the scleral ossicles of reptiles, which develop directly from ectomesenchyme (i.e., intramembranous ossification) and independently from the scleral cartilage
are of dermal (neural crest) origin, develop intramembranously within the scleral mesenchyme, and are induced to form by overlying (transient) epithelial scleral papillae (Nelson, 1942; Murray, 1943; Fyfe and Hall, 1981, 1983; Hall, 1981, 2005; Pinto and Hall, 1991)
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
Scleral papillae (which induce scleral ossicles in birds) have not been reported in teleosts, but evidence for their presence may not have been sought
The scleral ossicles are of dermal (neural crest) origin, develop intramembranously within the scleral mesenchyme, and are induced to form by overlying (transient) epithelial scleral papillae (Nelson, 1942; Murray, 1943; Fyfe and Hall, 1981, 1983; Hall, 1981, 2005; Pinto and Hall, 1991)
A single extraembryonic epithelium, which closes the germband dorsally.
May be obsoleted once added to insect ontology. Coordinate with cell type in CL
An epithelium that is part of a extraembryonic structure.
Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus.
epithelium stratificatum squamosum noncornificatum
nonkeratinizing stratified squamous epithelium
stratified squamous non-keratinized epithelium
stratified squamous nonkeratinizing epithelium
non-keratinized stratified squamous epithelium
The conjunctiva is divided into 3 parts.
The part of the conjunctiva, a thin transparent mucous membrane, that is loosely attached the orbital septum and covers the anterior surface of the sclera.
covers the eyeball, over the sclera. This region of the conjunctiva is tightly bound to the underlying sclera by Tenon's capsule and moves with the eyeball movements.
line of reflexion of the conjunctiva from the eyelid to the eyeball.
Forms the junction between the bulbar and palpebral conjunctivas. It is loose and flexible, allowing the free movement of the lids and eyeball
Scleral element located at the posterior pole of the scleral cartilage surrounding the foramen through which the optic nerve fibers pass. the internal architecture of this bone reveals a cancellous marrow cavity with fatty tissue.
At present, it has been documented in 219 species from 35 families, including perching birds, woodpeckers, hummingbirds, toucans, kingfishers, and falcons (Tiemeier, 1950). Morphologically, this element varies in shape from a complete encircling element in some woodpeckers (e.g., Melanerpes eryth- rocephalus) to an abbreviated arc in Gallus
An ossified element investing the upper eyelid.
PMID:16496288 says 'invests' the eyelid, is this consistent across taxa?
The most extreme development of the palpebral is found in the armored dino- saur Euoplocephalus tutus, where the bone forms a quarter-sphere and adducts to completely occlude the or- bit (Coombs, 1972; Vickaryous and Russell, 2003). Notwithstanding the superficially similar position, palpe- brals and tarsal plates differ both anatomically and developmentally and are not considered homologous (Gauthier et al., 1988)
thin cartilage element that stiffens the nictitating membrane.
these laminae may consist of purely hyaline cartilage (cats and horses) or may be heavily invested with elastic fibers (dogs, pigs, and cows; Schlegel et al., 2001)
Morphology notes: Generally, the cartilage consists of a long narrow appendix which is followed by a variable crossbar[PMID:11325064]
A sesamoid bone that lies adjacent to the tendon of one of the muscles responsible for adducting the nictitating membrane (the pyramidal nictitating muscle)
During contraction, the scleral sesamoid bone acts to anchor the pyramidal nictitating muscle to the sclera and divert the tendon from pro- jecting over the cornea. It remains to be determined whether this is indeed a true sesamoid (sensu; Vickaryous and Olson, 2006), as the scleral sesa- moid is actually invested within the synovial tendon sheath and not the tendon per se
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
obsolete germ layer / neural crest derived structure
A skeletal element that is part of a ocular region.
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
Cranial skeleton derived from neural crest cells.
permanent cartilage structure projecting from the site of origin of the recti muscles. Supports eyeball and aids rotation.
obsolete early digestive tract associated mesenchyme
Mesenchyme that is part of a limb/fin bud.
Mesenchyme that is part of a developing eyelid.
An epithelium that is part of a handplate.
Mesenchyme that is part of a extraembryonic membrane.
Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme.
maxillary process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme.
maxillary process mesenchyme from head mesenchyme
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme.
1st arch maxillary mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme.
head mesenchyme derived arch 2 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 2nd arch
pharyngeal arch 2 mesenchyme from head mesenchyme
branchial arch 2 mesenchyme from head mesenchyme
2nd arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme.
head mesenchyme derived arch 3 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 3rd arch
pharyngeal arch 3 mesenchyme from head mesenchyme
branchial arch 3 mesenchyme from head mesenchyme
3rd arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme.
head mesenchyme derived arch 4 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from head mesenchyme
branchial arch 4 mesenchyme from head mesenchyme
4th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
head mesenchyme derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from head mesenchyme
branchial arch 6 mesenchyme from head mesenchyme
6th arch mesenchyme from head mesenchyme
A otic capsule endochondral element that is composed primarily of a pre-cartilage condensation.
hyoid cartilage pre-cartilage condensation
Reichert's cartilage pre-cartilage condensation
The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&.
currently classified as a zone of a bone organ, but exists prior to bone ossifying
A primary ossification center is the first area of a bone to start ossifying. It usually appears during prenatal development in the central part of each developing bone. In long bones the primary centers occur in the diaphysis/shaft and in irregular bones the primary centers occur usually in the body of the bone. Most bones have only one primary center (e.g. all long bones) but some irregular bones such as the os coxa (hip) and vertebrae have multiple primary centers.
A secondary ossification center is the area of ossification that appears after the primary ossification center has already appeared - most of which appear during the postnatal and adolescent years. Most bones have more than one secondary ossification center. In long bones, the secondary centres appear in the epiphyses.
An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum
Note that humans do not have hemal arches, so VA=NA for FMA
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from neural crest
Partially implements UBERONREF:0000002 NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from head mesenchyme
pharyngeal arch mesenchyme from head mesenchyme
Nonsynovial joint in which the articulating bones are connected by bone. Examples: epiphyseal junction, manubriosternal synostosis.
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla.
in many vertebrates, odontoid tissue is not restricted to the teeth
Classified as a portion of organism substance in FMA
A vasculature that is part of a conjunctiva.
The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa.
A unit of lung supplied by three to five terminal bronchioles and contained by fibrous septa.
a pyramidal mass of lung tissue with sides that are bounded by the incomplete interlobular connective tissue septa and with a base, which is 1-2 cm in diameter, which usually faces the pleural surface of the lung; lobules that occupy a more central position in the lung are not well defined and are considered to consist of three to five pulmonary acini with proximate terminal bronchioles.
One of the veins of the lower leg; empty into the popliteal vein
Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea.
In the ethmoid bone, a curved lamina, the uncinate process, projects downward and backward from this part of the labyrinth; it forms a small part of the medial wall of the maxillary sinus, and articulates with the ethmoidal process of the inferior nasal concha.
In the head of the pancreas, the angle of junction of the lower and left lateral borders forms a prolongation, termed the uncinate process. During the embryonic development of the distal foregut, the duodenum c-shape is formed while rotating the ventral pancreatic bud into the dorsal bud. The dorsal and ventral pancreatic buds fuse. The dorsal pancreatic bud becomes the body, tail, and isthmus of the pancreas and the ventral pancreatic bud forms the pancreatic head and uncinate process[WP]
consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')
Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')
Mesenchyme that develops_from a somatopleure.
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
Mesenchyme that develops_from a splanchnopleure.
The superior tarsal muscle is a smooth muscle adjoining the levator palpebrae superioris muscle that helps to raise the upper eyelid.
declaring this to be both smooth muscle and part of the LPS leads to a disjointness violation (smooth muscle and striated muscle)
the neurons that innervate the esophagus, stomach, small and large bowel
A anatomical space that is enclosed by a hypopharynx.
A lymphoid follicle that is part of a Peyer's patch.
The Peyer's patch area normally occupied by T lymphocytes
The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID]
The proximal rib derives from the caudal half of somite[PMID:15906248]
A bone which corresponds to the inner plate of the pterygoid process of the human skull, but which, in all vertebrates below mammals, is not connected with the posterior nares, but serves to connect the palatine bones with the point of suspension of the lower jaw
In tetrapods, the pterygoid is a complex, but relatively stable, paired palatal bone with a number of parts. For the following discussion, it may be best to refer to the images of tetrapod palates at, for example Ornithosuchus, Therapsida, or Palatines. In many tetrapods, it is the largest palatal bone and serves as the main structural support. Most typically, the pterygoids meet extensively on the mid-line of the palate and jointly send a process, the palatal ramus, anteriorly, which may cover the parasphenoid more or less completely. Sometimes this term is used to include the main body of the pterygoid as well. More variably, there are one or two anterolateral processes which go by various names, such as ectopterygoid ramus. In many amniotes, the pterygoid develops a strong transverse process or transverse flange which forms a bar running laterally across the palate. The pterygoid also articulates with (where present) the dorsoventral supports for the palate: the epipterygoid (dorsal) and the basipterygoid process of the braincase. Finally, the pterygoid sends a long, robust quadrate ramus with complex curvature down (posteroventrally) to grasp the quadrate and support the jaw articulation. Basally, in fishes, the terminology tends to be a little different. Refer to the image of the Frasnian actinistian Diplocercides. The pterygoid bone of tetrapods is, roughly speaking, derived from the middle, entopterygoid (see also entry at entopterygoid for alternative definitions) portion of the palatoquadrate complex. The entopterygoid is not actually a part of the palatoquadrate. It is a dermal bone which has replaced the middle section of the primitively continuous endochondral bone of the palatoquadrate, the original upper jaw. In tetrapods, the pterygoid advances further, and also replaces the central part of the posterior, pterygoquadrate unit. This becomes the quadrate ramus. The upper part of this unit, the portion involved in the dorsal and basipterygoid articulations between jaw and braincase, is referred to as the metapterygoid. In tetrapods, most of this region is incorporated into the pterygoid as well, with the exception of the ascending process of the palatoquadrate, which becomes the epipterygoid. Since the anterior braincase articulation is lost in tetrapods, the only remaining sections of the palatoquadrate are the epipterygoid and the quadrate (or, in mammals, the incus). Everything else is either lost or is replaced by the pterygoid[Palaeos]
Palatal bones of intramembranous origin that lie anterior to the otic capsules, lateral to the orbits, and medial to the maxillae.[AAO]
lamina lateralis (processus pterygoideus)
lamina lateralis processi pterygoideus ossis sphenoidalis
Sources vary as to whether the pterygoid corresponds to the pterygoid processes in general, or the latter/inner plate.
An organ cavity that is part of a urethra.
The subserous connective tissue of the pelvic floor of the supracervical portion of the uterus. The parametrium extends laterally between the layers of the broad ligament.
subserous coat of the uterus laterally between the layers of the broad ligament[MP] - todo - check relationships
An unstimulated network of follicular dendritic cells and small resting B cells in the lymph node cortex.
Lymphatic vessel that enters the lymph node. The afferent lymph vessels enter at all parts of the periphery of the lymph node, and after branching and forming a dense plexus in the substance of the capsule, open into the lymph sinuses of the cortical part. In doing this they lose all their coats except their endothelial lining, which is continuous with a layer of similar cells lining the lymph paths
Lymphatic vessel that exits the lymph node. The efferent lymphatic vessel commences from the lymph sinuses of the medullary portion of the lymph nodes and leave the lymph nodes either to veins or greater nodes. Efferent lymphatic vessels are also found in the thymus and spleen. This is in contrast to afferent lymphatic vessels, which are found only in lymph nodes.
The border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood
Note that there is no consensus in the literature about which compartments constitute the white pulp or the ramifications of the microvasculature. In addition, notable differences exist between humans and rodents. In this ontology, the marginal sinus (which may not exist in human) has been included as part of the white pulp. The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents.
one of the branches of the splenic artery[MP]
When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia]
one of the veins that feed the splenic vein
The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia]
A blood vessel surrounded by the periarteriolar lymphoid sheath that connects the trabecular artery to the trabecular vein
The part of the future brain that is derived from the mantle layer of the neural tube
not clear if the MA/EMAPA classes refer specifically to the cortical subset. DHBA class incldues non-neocortex derivatives so it belongs here
A cell layer below the ependyma in the lateral ventricles of the brain. This region contains adult neural stem cells which have the potential to generate new neurons and glial cells via neurogenesis. It is an adult version of the embryonic forebrain germinal zone
Column of motor neurons which innervate muscles in the limb; motor neurons in the lateral motor column are further organized into pools, each of which innervates a specific muscle in the limb
nerve fibers that utilize acetylcholine as a neurotransmitter to the intestinal system
The angular artery is the terminal part of the facial artery; it ascends to the medial angle of the eye's orbit, imbedded in the fibers of the angular head of the Quadratus labii superioris, and accompanied by the angular vein.
encapsulated adipose tissue found in the groin
encapsulated adipose tissue found on the dorsal side of the peritoneum
encapsulated adipose tissue associated with the epididymis
encapsulated adipose tissue associated with the extension of the subserous coat of the uterus laterally between the layers of the broad ligament
encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon
dark-staining regions of layer four of the somatosensory cortex where somatosensory inputs from the contralateral side of the body come in from the thalamus. Barrels are found in some species of rodents and species of at least two other orders.
primary somatosensory area, barrel field
The term barrel field of the primary somatosensory area refers to one of 6 subdivisions of the primary somesthetic area of the cerebral cortex in the mouse ( Dong-2004 ) and the rat ( Swanson-2004 ). The other five are the lower limb of the primary somatosensory area, the mouth of the primary somatosensory area, the nose of the primary somatosensory area, the trunk of the primary somatosensory area and the upper limb of the primary somatosensory area. -- http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2703
A part of the lymph node cortex in which B lymphocytes home to primary follicles to survey follicular dendritic cells (FDCs); antigen stimulated B cells proliferate and differentiate within the follicles forming distinctive germinal centers
The paracortex and interfollicular cortex of the lymph node in which T lymphocytes home to survey dendritic cells
An orifice that is part of a lower urinary tract.
one of the tubular invaginations of the epidermis enclosing the hair roots and from which grow the vibrissae located on the muzzle and face of many species
A part of the secondary follicle in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these are displaced by the expanding germinal centre and form a 'mantle' around it
The area of the (spleen) secondary B follicle that surrounds the germinal center and harbors the small recirculating B lymphocytes
A lymphoid follicle containing naive B cells
The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles
A primary nodular lymphoid tissue that is part of a tonsil.
The distal rib derives from both somite halves[PMID:15906248]
opening/conduit between the nasal cavity and the oropharynx via the roof of the mouth.
todo - check AAO:0000025 apertura nasalis interna
Hole on the nasal capsule that connects the nasal and buccal cavites.[AAO]
has function in pressure equalization in birds that fly to high altitudes
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment, the bones are expanded into broad, flat plates, as in the cranium, the ilium, sternum, rib cage, the sacrum and the scapula. These bones are composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult, most red blood cells are formed in flat bones. In the cranial bones, the layers of compact tissue are familiarly known as the tables of the skull; the outer one is thick and tough; the inner is thin, dense, and brittle, and hence is termed the vitreous table. The intervening cancellous tissue is called the diploC+, and this, in certain regions of the skull, becomes absorbed so as to leave spaces filled with air (air-sinuses) between the two tables. The flat bones are: the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs.
One of: zygomaticus major, zygomaticus minor
A narrow, elongated muscle of the rotator cuff
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
glandular in NCIT; we consider the two NCIT terms synonymous
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
non-ciliated pseudostratified columnar epithelia
pseudostratified smooth columnar epithelium
The outermost of the two layers of the cranial dura mater which normally always adheres to the periosteum of the bones of the cranial vault
The inner layer of the dura mater surrounding the brain. It is mostly fused with the outer layer, the endocranium that is adherent to the inner aspect of the cranial bones. These two layers form the dura mater. The latter covers and protects the brain and the spinal cord.
not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area
The intracranial dura mater, consisting of two layers: the outer periosteal layer which normally always adheres to the periosteum of the bones of the cranial vault; and the inner meningeal layer which in most places is fused with the outer. The two layers separate to accommodate meningeal vessels and large venous (dural) sinuses. The meningeal layer is also involved in the formation of the various dural folds, such as the falx cerebri and tentorium cerebelli and is comparable to and continuous with the dural mater of the spinal cord. The cranial epidural space is then a potential space between the bone and the combined periosteum/periosteal layer of the dura mater realised only pathologically and is neither continuous with or comparable to the vertebral epidural space
A strand of hair that is part of a coat of hair.
A truncal hair that has a single constriction and bend about midway along the hair shaft, and contains two or more air cells in the medulla
A truncal hairs that is straight, but shorter than a guard hair, and contain two or more air cells in the medulla
A long, straight truncal hair that contains two air cells in the medulla[MP]. A strand of hair from the top layer consisting of longer, often coarser, straight shafts of hair that stick out through the underfur. This is usually the visible layer for most mammals and contains most of the pigmentation.
It protects the underfur from outside factors, such as rain, and is thus often water-repellent
A truncal hair that has two or more sharp bends with diameter constrictions at the bends, and contain one air cell in the medulla.
A strand of hair from the fine underhair of the coat
A layer of transparent, immovable disc-shaped skin or scale covering the eyes of some animals for protection, especially in animals without eyelids. The brille has evolved from a fusion of the upper and lower eyelids.
In snakes, there is no eyelid and the brille is clear and cannot be distinguished except when the animal is becoming ready for ecdysis. At that time, it becomes cloudy and is visible as a cover over the eye. When the snake moults, the brille is also shed as part of its skin. The Brilles protect their eyes from dust and dirt and gives them a 'glassy-eyed' blank appearance Snakes, flap-footed lizards, night lizards, and some skinks have brilles. All geckos except those in the subfamily Eublepharinae (eyelid geckos) possess brilles. Fish also have transparent eyelids called adipose eyelids.
there are transitional stages between total lid loss and full brille formation (Bellairs & Boyd, 1947).
A male anatomical structure found some groups of animals, used in mating. Male cartilaginous fish have claspers formed from the posterior portion of their pelvic fin which serve as intromittent organs used to channel semen into the female's cloaca during mating. The act of mating in some fish including sharks usually includes one of the claspers raised to allow water into the siphon through a specific orifice. The clasper is then inserted into the vagina, where it opens like an umbrella to anchor its position. The siphon then begins to contract expelling water and sperm. Male chimaeras have cephalic claspers on their heads, which are thought to aid in holding the female during mating
the term is also used for insect claspers, but we reserve it for the elasmobranchii structure
A mace-like spiny-headed rod found on the mid-dorsal surface of heads of male Holocephali. Thought to aid in holding the female during copulation.
The rod-like extension of the medial portion of the pelvic fin in male Elasmobranchii and Holocephali. Claspers are used as intromittent organs (not in clasping), the grooves on their facing surfaces together forming a tube for the transmission of sperm when the claspers are held together. The anterior proximal opening is called the apopyle, the posterior distal opening the rhipidion
An electric organ that is part of a tail.
An electric organ that is part of a head.
An organ that is capable of detecting electrical stimulus
Skeletal element that forms as a replacement or substitution of another element or tissue.
A portion of tissue that consists of a tube composed of epithelial cells that connects larger vessels.
The peroneus tertius (also known as fibularis tertius) is a muscle of the human body located in the lower limb. The muscle arises from the lower third of the anterior surface of the fibula; from the lower part of the interosseous membrane; and from an intermuscular septum between it and the peroneus brevis. The tendon, after passing under the superior extensor retinaculum of foot and inferior extensor retinaculum of foot in the same canal as the extensor digitorum longus, is inserted into the dorsal surface of the base of the metatarsal bone of the 5th digit. It is innervated by the deep fibular nerve. Its action is that of weak dorsiflexion of the ankle joint and to evert the foot at the ankle joint.
The peroneus brevis muscle (or fibularis brevis) lies under cover of the peroneus longus, and is a shorter and smaller muscle.
An organ cavity that surrounded_by a bone.
different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic.
nephrogenic interstitium of nephrogenic zone
cap mesenchyme of metanephros of urinary system
An epithelial tube that is fated to become a nephron.
The metanephric cortex is the outer region of the metanephros[GO].
Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells.
A primitive nephron that is part of a metanephros.
An appendage segment that is part of a limb/fin.
A pre-cartilage condensation that has_potential_to_develop_into a tarsal bone.
A cartilaginous condensation that has_potential_to_develop_into a tarsal bone.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified].
The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted].
Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]
Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus.
Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]
Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.
Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 1 mesenchyme.
hind limb digit 1 metatarsal pre-cartilage condensation
pedal digit I metatarsal pre-cartilage condensation
toe 1 metatarsal pre-cartilage condensation
foot digit 1 metatarsal pre-cartilage condensation
pedal digit 1 metatarsal pre-cartilage condensation
A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 2 mesenchyme.
hind limb digit 2 metatarsal pre-cartilage condensation
pedal digit II metatarsal pre-cartilage condensation
toe 2 metatarsal pre-cartilage condensation
foot digit 2 metatarsal pre-cartilage condensation
pedal digit 2 metatarsal pre-cartilage condensation
A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 3 mesenchyme.
hind limb digit 3 metatarsal pre-cartilage condensation
pedal digit III metatarsal pre-cartilage condensation
toe 3 metatarsal pre-cartilage condensation
foot digit 3 metatarsal pre-cartilage condensation
pedal digit 3 metatarsal pre-cartilage condensation
A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 4 mesenchyme.
hind limb digit 4 metatarsal pre-cartilage condensation
pedal digit IV metatarsal pre-cartilage condensation
toe 4 metatarsal pre-cartilage condensation
foot digit 4 metatarsal pre-cartilage condensation
pedal digit 4 metatarsal pre-cartilage condensation
A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 5 mesenchyme.
hind limb digit 5 metatarsal pre-cartilage condensation
pedal digit V metatarsal pre-cartilage condensation
toe 5 metatarsal pre-cartilage condensation
foot digit 5 metatarsal pre-cartilage condensation
pedal digit 5 metatarsal pre-cartilage condensation
A pedal digit metatarsal cartilage condensation that is part of a pedal digit 1 mesenchyme.
hind limb digit 1 metatarsal cartilage condensation
pedal digit I metatarsal cartilage element
foot digit 1 metatarsal cartilage element
pedal digit 1 metatarsal cartilage element
A pedal digit metatarsal cartilage element that is part of a pedal digit 2 mesenchyme.
hind limb digit 2 metatarsal cartilage condensation
pedal digit II metatarsal cartilage element
foot digit 2 metatarsal cartilage element
pedal digit 2 metatarsal cartilage element
A pedal digit metatarsal cartilage element that is part of a pedal digit 3 mesenchyme.
hind limb digit 3 metatarsal cartilage condensation
pedal digit III metatarsal cartilage element
foot digit 3 metatarsal cartilage element
pedal digit 3 metatarsal cartilage element
A pedal digit metatarsal cartilage element that is part of a pedal digit 4 mesenchyme.
hind limb digit 4 metatarsal cartilage condensation
pedal digit IV metatarsal cartilage element
foot digit 4 metatarsal cartilage element
pedal digit 4 metatarsal cartilage element
A pedal digit metatarsal cartilage element that is part of a pedal digit 5 mesenchyme.
hind limb digit 5 metatarsal cartilage element
pedal digit V metatarsal cartilage element
foot digit 5 metatarsal cartilage element
pedal digit 5 metatarsal cartilage element
Mesenchyme that is part of a developing pedal digit 1.
Mesenchyme that is part of a developing manual digit 1.
A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 1 mesenchyme.
finger 1 metacarpus pre-cartilage condensation
fore limb digit 1 metacarpus pre-cartilage condensation
manual digit I metacarpus pre-cartilage condensation
hand digit 1 metacarpus pre-cartilage condensation
manual digit 1 metacarpus pre-cartilage condensation
A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 2 mesenchyme.
finger 2 metacarpus pre-cartilage condensation
fore limb digit 2 metacarpus pre-cartilage condensation
manual digit II metacarpus pre-cartilage condensation
hand digit 2 metacarpus pre-cartilage condensation
manual digit 2 metacarpus pre-cartilage condensation
A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 3 mesenchyme.
finger 3 metacarpus pre-cartilage condensation
fore limb digit 3 metacarpus pre-cartilage condensation
manual digit III metacarpus pre-cartilage condensation
hand digit 3 metacarpus pre-cartilage condensation
manual digit 3 metacarpus pre-cartilage condensation
A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 4 mesenchyme.
finger 4 metacarpus pre-cartilage condensation
fore limb digit 4 metacarpus pre-cartilage condensation
manual digit IV metacarpus pre-cartilage condensation
hand digit 4 metacarpus pre-cartilage condensation
manual digit 4 metacarpus pre-cartilage condensation
A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 5 mesenchyme.
finger 5 metacarpus pre-cartilage condensation
fore limb digit 5 metacarpus pre-cartilage condensation
manual digit V metacarpus pre-cartilage condensation
hand digit 5 metacarpus pre-cartilage condensation
manual digit 5 metacarpus pre-cartilage condensation
A manual digit metacarpus cartilage element that is part of a manual digit 1 mesenchyme.
fore limb digit 1 metacarpus cartilage element
manual digit I metacarpus cartilage element
hand digit 1 metacarpus cartilage element
manual digit 1 metacarpus cartilage element
A manual digit metacarpus cartilage element that is part of a manual digit 2 mesenchyme.
fore limb digit 2 metacarpus cartilage element
manual digit II metacarpus cartilage element
hand digit 2 metacarpus cartilage element
manual digit 2 metacarpus cartilage element
A manual digit metacarpus cartilage element that is part of a manual digit 3 mesenchyme.
fore limb digit 3 metacarpus cartilage element
manual digit III metacarpus cartilage element
hand digit 3 metacarpus cartilage element
manual digit 3 metacarpus cartilage element
A manual digit metacarpus cartilage element that is part of a manual digit 4 mesenchyme.
finger 4 metacarpus cartilage condensation
fore limb digit 4 metacarpus cartilage element
manual digit IV metacarpus cartilage element
hand digit 4 metacarpus cartilage element
manual digit 4 metacarpus cartilage element
A manual digit metacarpus cartilage element that is part of a manual digit 5 mesenchyme.
finger 5 metacarpus cartilage condensation
fore limb digit 5 metacarpus cartilage element
manual digit V metacarpus cartilage element
hand digit 5 metacarpus cartilage element
manual digit 5 metacarpus cartilage element
A pre-cartilage condensation that is part of a manual digit 1 mesenchyme.
fore limb digit 1 phalanx pre-cartilage condensation
manual digit I phalanx pre-cartilage condensation
hand digit 1 phalanx pre-cartilage condensation
manual digit 1 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a manual digit 2 mesenchyme.
fore limb digit 2 phalanx pre-cartilage condensation
manual digit II phalanx pre-cartilage condensation
hand digit 2 phalanx pre-cartilage condensation
manual digit 2 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a manual digit 3 mesenchyme.
fore limb digit 3 phalanx pre-cartilage condensation
manual digit III phalanx pre-cartilage condensation
hand digit 3 phalanx pre-cartilage condensation
manual digit 3 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a manual digit 4 mesenchyme.
fore limb digit 4 phalanx pre-cartilage condensation
manual digit IV phalanx pre-cartilage condensation
hand digit 4 phalanx pre-cartilage condensation
manual digit 4 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a manual digit 5 mesenchyme.
fore limb digit 5 phalanx pre-cartilage condensation
manual digit V phalanx pre-cartilage condensation
hand digit 5 phalanx pre-cartilage condensation
manual digit 5 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit 1 mesenchyme.
hind limb digit 1 phalanx pre-cartilage condensation
pedal digit I phalanx pre-cartilage condensation
foot digit 1 phalanx pre-cartilage condensation
pedal digit 1 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit 2 mesenchyme.
hind limb digit 2 phalanx pre-cartilage condensation
pedal digit II phalanx pre-cartilage condensation
foot digit 2 phalanx pre-cartilage condensation
pedal digit 2 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit 3 mesenchyme.
hind limb digit 3 phalanx pre-cartilage condensation
pedal digit III phalanx pre-cartilage condensation
foot digit 3 phalanx pre-cartilage condensation
pedal digit 3 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit 4 mesenchyme.
hind limb digit 4 phalanx pre-cartilage condensation
pedal digit IV phalanx pre-cartilage condensation
foot digit 4 phalanx pre-cartilage condensation
pedal digit 4 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit 5 mesenchyme.
hind limb digit 5 phalanx pre-cartilage condensation
pedal digit V phalanx pre-cartilage condensation
foot digit 5 phalanx pre-cartilage condensation
pedal digit 5 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit mesenchyme.
hind limb digit phalanx pre-cartilage condensation
hindlimb phalanx pre-cartilage condensation
foot digit phalanx pre-cartilage condensation
pedal digit phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a manual digit mesenchyme.
fore limb digit phalanx pre-cartilage condensation
forelimb phalanx pre-cartilage condensation
manus phalanx pre-cartilage condensation
hand digit phalanx pre-cartilage condensation
manual digit phalanx pre-cartilage condensation
A cartilage element that is part of a manual digit 1 mesenchyme.
fore limb digit 1 phalanx cartilage condensation
manual digit I phalanx cartilage element
manual digit 1 phalanx cartilage element
A cartilage element that is part of a manual digit 2 mesenchyme.
fore limb digit 2 phalanx cartilage condensation
manual digit II phalanx cartilage element
manual digit 2 phalanx cartilage element
A cartilage element that is part of a manual digit 3 mesenchyme.
fore limb digit 3 phalanx cartilage condensation
manual digit III phalanx cartilage element
manual digit 3 phalanx cartilage element
A cartilage element that is part of a manual digit 4 mesenchyme.
fore limb digit 4 phalanx cartilage condensation
manual digit IV phalanx cartilage element
manual digit 4 phalanx cartilage element
A cartilage element that is part of a manual digit 5 mesenchyme.
fore limb digit 5 phalanx cartilage condensation
manual digit V phalanx cartilage element
manual digit 5 phalanx cartilage element
A cartilage element that is part of a pedal digit 1 mesenchyme.
hind limb digit 1 phalanx cartilage condensation
A cartilage element that is part of a pedal digit 2 mesenchyme.
hind limb digit 2 phalanx cartilage condensation
pedal digit II phalanx cartilage element
A cartilage element that is part of a pedal digit 3 mesenchyme.
hind limb digit 3 phalanx cartilage condensation
pedal digit III phalanx cartilage element
A cartilage element that is part of a pedal digit 4 mesenchyme.
hind limb digit 4 phalanx cartilage condensation
pedal digit IV phalanx cartilage element
A cartilage element that is part of a pedal digit 5 mesenchyme.
hind limb digit 5 phalanx cartilage condensation
A cartilage element that is part of a pedal digit mesenchyme.
hind limb digit phalanx cartilage condensation
A cartilage element that is part of a manual digit mesenchyme.
fore limb digit phalanx cartilage condensation
hand digit phalanx cartilage condensation
hind limb digit metatarsal pre-cartilage condensation
metatarsal bone pre-cartilage condensation
foot digit metatarsal pre-cartilage condensation
pedal digit metatarsal pre-cartilage condensation
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified].
An epithelium that is part of a manual digit 1.
An epithelium that is part of a pedal digit 1.
Mesenchyme of the carpal region that conributes to the tarsal skeleton.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm].
EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton
hind limb digit metatarsal cartilage condensation
foot digit metatarsal cartilage condensation
pedal digit metatarsal cartilage element
fore limb digit metacarpus pre-cartilage condensation
metacarpal bone pre-cartilage condensation
hand digit metacarpus pre-cartilage condensation
manual digit metacarpus pre-cartilage condensation
fore limb digit metacarpus cartilage element
manual digit metacarpus cartilage element
The collection of all skeletal elements in an forelimb zeugopod region.
adding proxinally_connected_to humerus causes inconsistencies - requires investigation
Segment of the forearm corresponding to the radius and ulna.[AAO]
A liver parenchyma that is part of a quadrate lobe of liver.
A liver parenchyma that is part of a caudate lobe of liver.
An organism subdivision that includes both an appendage and its accociated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] AO notes: note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.
Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)
pectoral girdle plus anterior limb or fin
pectoral girdle plus pectoral limb or fin
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here
pelvic girdle plus posterior limb or fin
Paired fin skeleton that consists of the supporting endochondral proximal and distal radials and the dermal fins rays or lepidotrichia. The pectoral fin skeleton is located in the thoracic region of the body and articulates with the scapula and coracoid.
Paired fin skeleton located in the abdominal position that consists of supporting endochondral radialsB and dermal fin rays or lepidotrichia.
the girdle is part of the pelvic fin skeleton in ZFA - needs resolved
Skeletal subdivision that is a segment of the limb skeleton.
note the distinction between this and skeleton of limb
The collection of all skeletal elements in a single paired fin.
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[VSAO]
A iliac endochondral element that is composed primarily of a cartilage tissue.
A pubic endochondral element that is composed primarily of a cartilage tissue.
The subdivision of the skeleton of either the pectoral or pelvic girdle.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula.
Segment of the leg corresponding to the tibia and fibula.[AAO]
There are three cuneiform bones in the human foot: the medial cuneiform the intermediate cuneiform also known as the middle the lateral cuneiform. They are located between the navicular bone and the first, second and third metatarsal bones and are medial to the cuboid bone[WP, unvetted, human specific].
Series of elements that articulate with the metatarsals.[AAO]
A bone which does not occur frequently in the body but is still present in a significantly large number of organisms
An accessory bone located proximal to the base of the fifth metatarsal. Its prevalence has been reported to be from 0.1% to 1.0%. This bone is found within the peroneus brevis tendon and is considered to be asymptomatic in the majority of people
An accessory bone tubercle which if present lies posterior to the talus
An accessory bone of the pes that occasionally develops abnormally in front of the ankle towards the inside of the pes. This bone may be present in approximately 2.5% of the general population and is usually asymptomatic
A piece of bone that is located within a suture in the cranium.
A orbitosphenoid endochondral element that is composed primarily of a pre-cartilage condensation.
sphenoid lesser wing pre-cartilage condensation
A alisphenoid endochondral element that is composed primarily of a pre-cartilage condensation.
sphenoid greater wing pre-cartilage condensation
A alisphenoid endochondral element that is composed primarily of a cartilage tissue.
sphenoid greater wing cartilage condensation
Endochondral tarsal bone articulating with centralia and metatarsal 4.
We need to restrict the logical definition such that it is *only* connecting to metatarsal 4
Small element that articulates anteriorly with metatarsal IV. It may be absent in some taxa.[AAO]
Endochondral tarsal bone articulating with centralia and metatarsal 5.
Small element that articulates anteriorly with metatarsal V. It may be absent in some taxa.[AAO]
We need to restrict the logical definition such that it is *only* connecting to metatarsal 5
endochondral carpal bone similar to distal carpal 4, but lost in most reptiles and mammals.
Small element that articulates anteriorly with metacarpal IV(V). It may be fused to carpal 4(3), 5(4), the ulnare, radiale, or other elements.[AAO]
lost in most reptiles and mammals[VSAO]. Small element that articulates anteriorly with metacarpal IV(V). It may be fused to carpal 4(3), 5(4), the ulnare, radiale, or other elements
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin.
considering adding pectoral and pelvic complex skeleton classes
note that the MA class includes girdle parts so it belongs here;
bone of forelimb or pectoral fin or pectoral girdle
A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle
The collection of all meningeal layers that line a central nervous system.
In some primitive organisms, the meningeal cluster includes only the primitive meninx
A sacral vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
sacral vertebral pre-cartilage condensation group
sacral vertebra pre-cartilage condensation
A sacral vertebra endochondral element that is composed primarily of a cartilage tissue.
sacral vertebral cartilage condensation group
The extension of the ilium above the level of the acetabulum. Attachment site for both hindlimb and caudal musculature. Medially is the site of attachment of the sacral ribs, where these exist[PHENOSCAPE:ad].
The body of ilium enters into the formation of the acetabulum, of which it forms rather less than two-fifths. Its external surface is partly articular, partly non-articular; the articular segment forms part of the lunate surface of the acetabulum, the non-articular portion contributes to the acetabular fossa. The internal surface of the body is part of the wall of the lesser pelvis and gives origin to some fibers of the Obturator internus. Below, it is continuous with the pelvic surfaces of the ischium and pubis, only a faint line indicating the place of union.
A lymphoid follicle that is part of a lymph node.
The middle pharyngeal constrictor is a fanshaped muscle, smaller than the Inferior pharyngeal constrictor muscle.
The middle constrictor is a pharyngeal arches 4/6 muscle that participates in oral/pharyngeal behaviors and is innervated by the pharyngeal plexus of Vagus and attaches to the hyoid apparatus and the midline raphe.[FEED]
A bone separating the lacrimal and frontal bones in many tetrapod skulls
It first evolved in the sarcopterygian clade Rhipidistia, which includes lungfish and the Tetrapodomorpha. The prefrontal is found in most modern and extinct lungfish, amphibians and reptiles. It is very small, fused to the frontals or lost in many groups of coelurosaurian theropod dinosaurs and is completely absent in their modern descendants, the birds. The prefrontal was also lost in early mammaliaforms and so is not present in modern mammals either
squamous part of temporal bone primordium
A exoccipital endochondral element that is composed primarily of a cartilage tissue.
A secondary follicle that is located in a lymph node
A collection of activated B cells at the center of a secondary follicle, formed after B cells become activated and migrate to the center.
A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation.[GO]
The part of the secondary follicle that surrounds the germinal center.
consider making terminology consistent amongst subclasses - see http://purl.obolibrary.org/obo/uberon/tracker/7
The enmeshed group of antigen presenting cells with extensive dendritic processes in the spleen B cell follicle that present antigen to B cells during an immune response
splenic follicular dendritic cell network
The follicular dendritic cell network is often visualized by using the monoclonal antibody FDC-M2.
spleen follicular dendritic cell network
Typically a false rib in humans but may sometimes be a true one due to sternal attachment
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
subdivision of organism along appendicular axis
lies on the palmar aspect of the coffin joint between the second phalanx and third phalanx. articulates closely with the distal phalanx, to which it is connected by the impar ligament of the navicular bone. The impar ligament is very strong and permits relatively little motion between the navicular bone and the distal phalanx.
The supraglenoid tubercle is a region of the scapula to which the long head of the biceps brachii muscle attaches.
A calcaneum endochondral element that is composed primarily of a pre-cartilage condensation.
A calcaneum endochondral element that is composed primarily of a cartilage tissue.
A cartilaginous condensation that has_potential_to_develop_into a clavicle.
A pre-cartilage condensation that has_potential_to_develop_into a clavicle.
A pre-cartilage condensation that has_potential_to_develop_into a radius bone.
still to decide whether this is a distinct pre-cartilage condensation
A pre-cartilage condensation that has_potential_to_develop_into a ulna.
A radius-ulna endochondral element that is composed primarily of a cartilage tissue.
note that this is not represented as a single unit in EHDAA2
A cartilaginous condensation that has_potential_to_develop_into a tibia.
A pre-cartilage condensation that has_potential_to_develop_into a tibia.
A cartilaginous condensation that has_potential_to_develop_into a fibula.
A pre-cartilage condensation that has_potential_to_develop_into a fibula.
A smooth, rounded eminence on the lateral portion of the articular surface of the humerus. It articulates with the cupshaped depression on the head of the radius, and is limited to the front and lower part of the bone.
In birds, where forelimb anatomy has adaptation for flight, its functional if not ontogenetic equivalent is the dorsal condyle of the humerus
The Capitulum humeri is present in Carnivora, more distinctly in the cat than in the dog. The Fossa coronoidea, present in the cat is medial to the Fossa radialis and accommodates the Processus coronoideus medialis ulnae when the elbow is flexed. A Foramen supratrochleare occurs in carnivora and occasionally in pig.[NOMINA ANATOMICA VETERINARIA (2005)]
A skin of neck that is part of a throat.
A zone of skin that is part of a forelimb wing.
A membranous extension of skin that forms the wing material in animals such as bats. It typically comprises a number of patagial segments, stretching from the side of the body between the forelimb digits and sometimes the hindlimbs.
Examples - region between digits in a human embryo; segments of a bat's patagium
In bats and pterosaurs, thin web of skin that extends from the shoulder to the wrist anterior to the upper arm and forearm, and is fixed on the neck or skull.
In bats: The patagium present from the neck to the first digit
In birds: The triangular fold of skin on leading edge of the wing
In pterosaurs: the patagium present from the shoulder to the wrist
An interdigital region that is part of a patagium.
In bats: the portion found within the digits
A dactylopatagium that is connected_to a manual digit 1 and connected_to a manual digit 2.
A dactylopatagium that is connected_to a manual digit 2 and connected_to a manual digit 3.
A dactylopatagium that is connected_to a manual digit 3 and connected_to a manual digit 4.
A dactylopatagium that is connected_to a manual digit 4 and connected_to a manual digit 5.
A flight membrane running between the body and the limb or digits.
In bats: the portion found between the last digit (5) and the hindlimbs
In pterosaurs: Brachiopatagium: the portion stretching from the fourth finger to the hindlimbs
The membrane that is stretches between the legs of bats, used for flight, and in the case of insect-eating bats, for catching prey.
In bats: the posterior portion of the body between the two hindlimbs
In pterosaurs: Uropatagium or cruropatagium: the anterior portion between the two hindlimbs, depending on whether it did or did not include the tail
A spur of cartilage arising from inner side of ankle and running along part of outer interfemoral membrane in bats
to help spread the interfemoral membrane which is part of the wing membrane between the tail and the hind legs.
A calcareous tooth that is elongated and protrudes from the mouth.
Elongated, continuously growing front teeth, usually but not always in pairs, that protrude well beyond the mouth of certain mammal species. They are most commonly canines, as with warthogs, pig, and walruses, or, in the case of elephants and narwhals, elongated incisors. In most tusked species both the males and the females have tusks although the males are larger. Tusks are generally curved, though the narwhal's sole tusk is straight and has a helical structure. In the elephant, the tusks were originally second incisors. Continuous growth is enabled by formative tissues in the apical oproperty_value external_definitionof the roots of the teeth
A transverse fold of skin across the throat (Peters 1964).
A cartilaginous condensation that has_potential_to_develop_into a limb bone.
A pre-cartilage condensation that has_potential_to_develop_into a limb bone.
A cartilaginous condensation that has_potential_to_develop_into a forelimb bone.
forelimb wing cartilaginous condensation
A pre-cartilage condensation that has_potential_to_develop_into a forelimb bone.
forelimb bone pre-cartilage condensation
A cartilaginous condensation that has_potential_to_develop_into a hindlimb bone.
A pre-cartilage condensation that has_potential_to_develop_into a hindlimb bone.
hindlimb bone pre-cartilage condensation
A small pointed eminence of the external ear, situated in front of the concha, and projecting backward over the meatus.
The tragus is generally believed to play a role in vertical sound localization in bats
A hair-like unicellular external process of the body wall or any derivative of the latter; a hair; a bristle.
Obsoleted as the term 'seta' refers to a variety of different structures. For insect chaetae, consider the arthropod anatomy ontology.
either of two lateral parts of the ethmoid bone that form part of the anterior wall of the orbit
In avians, the mesethmoid supports upper beak formation
Muscles of the pelvic girdle, hindlimb or pelvic fin.
Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]
A muscle of a pectoral girdle, pectoral fin or anterior limb.
the MA class belongs here, based on its current child classes
Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]
An endochondral element of the nasal capsule that forms septum between nasal capsules and usually remains unossified in mammals
Endochondral ossification of the anteromedial portion of the braincase.[AAO]
absent in primitive mammals, ungulates, amphibians, reptiles/birds
A external naris that intersects the midsagittal plane of a head.
The hagfish's jawless mouth contains two parallel rows of pointed keratinous teeth
Hermaphroditic organism that produces gametes first of one sex, and then later of the other sex.
composed of lamprin, an elastin-like protein, unique to lampreys
Dermal element that arises via intramembranous ossification and are developmentally distinct from true ribs that articulate with the vertebral column.
These bones may have been derived from the ventral scales found in animals like rhipidistians, labyrinthodonts, and Acanthostega, and may be related to ventral elements of turtle plastrons
Hermaphroditic organism that produces both male and female gametes at the same time.
A cartilaginous condensation that has_potential_to_develop_into a tarsometatarsus.
A pre-cartilage condensation that has_potential_to_develop_into a tarsometatarsus.
tarsometatarsus pre-cartilage condensation
A cartilaginous condensation that has_potential_to_develop_into a tibiotarsus.
A pre-cartilage condensation that has_potential_to_develop_into a tibiotarsus.
lateral part derives from a fish dermal bone while the medial part comes from a spur off the manubrium endochondral bone[JB]
third bone of the lower leg, normally restricted to the area of the knee, in multuberculates, monotremes and some therians
An arrowhead-shaped bone in the avian hyoid apparatus which forms the base of the tongue
Posterior ossification of the otic capsule.
teleost fishes have a bone which is called the opisthotic. However, it is not homologous to the tetrapod opisthotic and the teleost otic capsule is all of a piece
see TAO:0000474 - intercalar "Small membrane bone homologous with a cartilage bone in more basal fishes (Patterson, 1977). Situated between the exoccipital and the pterotic at point of attachment of short ligament that originates on the ventral arm of the posttemporal."
Skeletal element that is often isolated, small, and variable in composition.
Ossicles are composed of a combination skeletal tissues, including bone, calcified cartilage, hyaline cartilage, etc, and exhibit variable development across species. Ossicles are not necessarily jointed, and examples include the menisci of synovial joints, 'Panda's thumb' (radial sesamoid), cardiac skeletal elements, sclerotic bones, middle ear ossicles, and sesamoids.
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Skeletal element that forms around the notochord and is part of the vertebral column.
we include a distinct subclass for bony vertebra
The middle thicker part of the thyrohyoid membrane is termed the median thyrohyoid ligament (middle hyothyroid ligament, middle thyrohyoid ligament), its lateral thinner portions are pierced by the superior laryngeal vessels and the internal branch of the superior laryngeal nerve. Its anterior surface is in relation with the Thyreohyoideus, Sternohyoideus, and Omohyoideus, and with the body of the hyoid bone
The lateral thyrohyoid ligament (lateral hyothyroid ligament) is a round elastic cord, which forms the posterior border of the hyothyroid membrane and passes between the tip of the superior cornu of the thyroid cartilage and the extremity of the greater cornu of the hyoid bone. The recurrent laryngeal nerve typical lies lateral to this ligament
fibers of the thyroarytenoid muscle that continue to the margin of the epiglottis; it closes the inlet to the larynx.
pars thyroepiglottica (musculus thyroarytenoideus)
pars thyroepiglottica musculus thyroarytenoidei
thyro-epiglottic part of thyro-arytenoid
pars thyroepiglottica musculi thyroarytenoidei
The part of the Inferior pharyngeal constrictor muscle that arises from cricoid cartilage
The cricopharyngeus is a pharyngeal arch 4/6 muscle that participates in oral/pharyngeal behaviors and is innervated by the pharyngeal plexus and the recurrent laryngeal n. , and is an integral part of the pharyngeal tube, and attaches to the cricoid cartilage and the midline raphe. It acts as a sphincter between the pharynx and esophagus.[FEED]
cricopharyngeal part of inferior constrictor pharyngeus
cricopharyngeal part of inferior pharyngeal constrictor
cricopharyngeal part of inferior pharyngeal constrictor muscle
cricopharyngeus portion of the inferior pharyngeal constrictor
pars cricopharyngea (musculus constrictor pharyngis inferior)
pars cricopharyngea musculus constrictoris pharyngis inferioris
may be obsoleted. Muscle between hyoid arches in fish;
One of the principal muscles used in swallowing.[AAO]
most extant actinopterygians part of the interhyoideus separates into a distinct muscle during development, the hyohyoideus - http://www.biomedcentral.com/1471-213X/8/24/
the [mammalian] interhyoideus is homologous with the simple interhyoideus of early stages of amphibia[Edgeworth, 1935]
Is a mandibular muscle that develops into the ventral intermandibularis anterior and posterior muscles.
Cricoarytenoid muscles are muscles that connect the cricoid cartilage and arytenoid cartilage. More specifically, it can refer to: Posterior cricoarytenoid muscle Lateral cricoarytenoid muscle
candidate for obsoletion. See https://github.com/obophenotype/uberon/issues/530
The orbicularis oris is a superficial facial muscle with fibers that encircle the opening of the oral cavity that attaches to the maxilla, mandible, skin and modiolus, and that participates in oral/pharyngeal behaviors, and is innervated by the facial nerve (CN VII).
The orbicularis oris is a superficial facial muscle that attaches to the skin and modiolus, and that participates in oral/pharyngeal behaviors, and is innervated by the facial nerve .[FEED]
pars thyropharyngea (musculus constrictor pharyngis inferior)
pars thyropharyngea musculus constrictoris pharyngis inferioris
thyropharyngeal part of inferior constrictor pharyngeus
thyropharyngeal part of inferior constrictor pharyngeus muscle
thyropharyngeal part of inferior pharyngeal constrictor
The salpingopharyngeus muscle arises from the inferior part of the cartilage of the pharyngotympanic tube (Eustachian tube) in the nasal cavity; it passes downward and blends with the posterior fasciculus of the palatopharyngeus muscle. The salpingopharyngeus is known to raise the pharynx and larynx during deglutition (swallowing) and laterally draws the pharyngeal walls up. In addition, it opens the pharyngeal orifice of the pharyngotympanic tube during swallowing. This allows for the equalization of pressure between the auditory canal and the pharynx. The salpingopharyngeus is innervated by the vagus nerve (CN X) via the pharyngeal plexus.
Salpingopharyngeus is a muscle that attaches to pharyngotympanic tube and the pharynx and is innervated by pharyngeal plexus of CN X and participates in oral/pharyngeal behaviors.[FEED]
The deep masseter is a separable part of the masseter muscle that attaches to lateral surface and/or ventral border of zygomatic arch.[FEED]
The zygomaticomandibularis is a separable part of the masseter muscle that attaches to the medial surface of the zygomatic arch.[FEED]
Either of the two muscles that comprise the digastric group (anterior or posterior).
FMA represents this as a muscle belly, but this classification does not work well across mammals (pers. comm., FEED:rd), so we classify this is a distinct muscle organ here.
The anterior digastric is a pharyngeal arch I muscle that participates in oral/pharygeal behaviors and is innervated by the nerve to mylohyoid (a branch of the third division of the trigeminal nerve), is attached to the mandible and to the hyoid apparatus, and it is superficial to mylohyoid muscle.
The anterior digastric is a pharyngeal arch I muscle that participates in oral/pharygeal behaviors and is innervated by the nerve to mylohyoid and superficial to mylohyoid muscle, and lacks the midline raphe.[FEED]
The posterior digastric is a pharyngeal arch II muscle that participates in oral pharyngeal behavior, is innervated by the digastric branchi of facial nerve and attaches to the posterior cranial base.[FEED]
in orangutans, this muscle attaches to the mandible rather than the hyoid
runs from the processus jugularis to the os stylohyoideum; innervated with the ramus jugulohyoideus from the nervus facialis
The occipitofrontalis or epicranius is a muscle which covers parts of the skull. It consists of two parts or bellies: The occipital belly, near the occipital bone, and the frontal belly, near the frontal bone.
A belly of the occipitofrontalis muscle that is near the occipital bone
venter occipitalis (musculus occipitofrontalis)
venter transversa musculus occipitofrontalis occipitalis
A muscle organ that attaches_to a clavicle and attaches_to a occipital bone.
Some studies have indicated a supernumerary cleido-occipital muscle more or less separate from the sterno-cleido-mastoid muscle; The frequency of cleido-occipital muscle occurrence has been reported up to 33%
A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum.
An occasional small muscle extending from the root of the styloid process to the cartilage of the meatus of the ear
A muscle that attaches to the base of the ear and to the middle of the skull
A belly of the occipitofrontalis muscle that is near the frontal bone
venter frontalis (musculus occipitofrontalis)
venter frontalis musculus occipitofrontalis
frontal belly of occipitofrontalis muscle
venter frontalis musculi occipitofrontalis
The nasalis (compressor naris) is a sphincter-like muscle of the nose whose function is to compress the nasal cartilage. It consists of two parts, transverse and alar: The transverse part arises from the maxilla, above and lateral to the incisive fossa; its fibers proceed upward and medially, expanding into a thin aponeurosis which is continuous on the bridge of the nose with that of the muscle of the opposite side, and with the aponeurosis of the Procerus. The alar part is attached at one end to the greater alar cartilage, and at the other to the integument at the point of the nose. Other sources divide it into 'Compressor nasalis' and 'Dilator nasalis'.
The ceratohyoideus is a muscle of Pharyngeal Arch III that participates in oral/pharyngeal behaviors and is innervated by the glossopharyngeal n. , and attaches to the ceratohyal part of the hyoid apparatus and also to a non-ceratohyal part of the hyoid apparatus.[FEED]
pars pterygopharyngea (musculus constrictor pharyngis superior)
pterygopharyngeal part of superior constrictor pharyngeus
pterygopharyngeal part of superior pharyngeal constrictor
A single muscle, filling up the posterior concave surfaces of the arytenoid cartilages. It arises from the posterior surface and lateral border of one arytenoid cartilage, and is inserted into the corresponding parts of the opposite cartilage. It consists of oblique and transverse parts.
A muscle organ that is part of a craniocervical region.
The transversospinal muscles are a group of muscles of the human back. Their combined action is rotation and extension of the vertebral column. They include: semispinalis, spanning 4-6 vertebral segments semispinalis dorsi semispinalis cervicis semispinalis capitis multifidus, spanning 2-4 vertebral segments rotatores, spanning 1-2 vertebral segments rotatores cervicis rotatores thoracis rotatores lumborum
A a triangular eminence projecting forward from the proximal epiphysis of the ulna[WP,modified].
A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints.
A cartilage element that is part of a splanchnocranium.
An endocardium that is part of a atrium auricular region.
EHDAA2 this is an epithelium that is part of the endocardium
An endocardium that is part of a left atrium auricular region.
left atrium auricular region endocardium
An endocardium that is part of a right atrium auricular region.
Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus.
The flexor pollicis brevis is a muscle in the hand that flexes the thumb. It is one of three thenar muscles. It has both a superficial part and a deep part.
The spinalis is the portion of the erector spinae, a bundle of muscles and tendons, located nearest to the spine. It is divided into three parts. [WP,unvetted].
Origin: spines of upper thoracic and lower cervical vertebrae; insertion: occipital bone; innervation: spinal nerves; action, extends head.
The pyramidalis is a small and triangular muscle, anterior to the Rectus abdominis, and contained in the rectus sheath.
A transversospinalis muscle of the human body.
A muscle that originates from the cuboid bone and divides into two portions, which are inserted into the medial and lateral sides of the base of the first phalanx of the great toe, a sesamoid bone being present in each tendon at its insertion.
The extrinsic extensor muscles of the hand are located in the back of the forearm and have long tendons connecting them to bones in the hand, where they exert their action.
The aryepiglotticus is a muscle of the larynx running in the aryepiglottic fold from the arytenoid cartilage to the epiglottis.
ary-epiglottic part of oblique arytenoid
pars aryepiglottica (musculus arytenoideus obliquus)
pars aryepiglottica musculus arytenoidei obliqui
pars aryepiglottica musculi arytenoidei obliqui
One of: obturator externus or obturator internus
The obturator internus muscle originates on the medial surface of the obturator membrane, the ischium near the membrane, and the rim of the pubis. It exits the pelvic cavity through the lesser sciatic foramen. The obturator internus is situated partly within the lesser pelvis, and partly at the back of the hip-joint. It functions to help laterally rotate extended thigh and abduct flexed thigh, as well as to steady the femoral head in the acetabulum.
Originates on the entire lateral surface of the pelvic rim. Dorsal fibers insert distally to the dorso-medial surface of the caput femoris and ventral fibers extend around the acetabulum to insert on the tendon of the caput femoris.[AAO]
Definition generalized to accommodate AAO class - 'Originates on the entire lateral surface of the pelvic rim. Dorsal fibers insert distally to the dorso-medial surface of the caput femoris and ventral fibers extend around the acetabulum to insert on the tendon of the caput femoris.' [AAO:0010052]
The peritoneum over the rectum and the bladder is continued over the intestinal surface and fundus of the uterus on to its vesical surface, which it covers as far as the junction of the body and cervix uteri, and then to the bladder, forming here a second, but shallower, pouch, the vesicouterine excavation (or uterovesical pouch). The vesicouterine excavation is close to the anterior fornix of the vagina.
A channel containing perilymph passing through the temporal bone, connecting the scala tympani of the cochlea to the subarachnoid space.
Duct that contains perilymph[ZFA:0005461, ZFIN:curator].
Dermal bone that is located posterior to the dentary and lateral to the articular and retroarticular bones of the lower jaw. The angular forms the outer dermal sheet of the posterior part of the lower jaw. The angular bears a portion of the mandibular sensory canal. The angular is a paired bone.
The angular fuses with the articular bone in clupeocephalans forming the anguloarticular.
The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG].
A ligament that is part of a knee joint.
A skeleton of pelvic girdle that is part of a right pelvic girdle region.
A skeleton of pelvic girdle that is part of a left pelvic girdle region.
A pelvic girdle region that is in the right side of a multicellular organism.
A pelvic girdle region that is in the left side of a multicellular organism.
A cartilage element that is part of a vertebral column.
This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups
A pre-cartilage condensation that is part of a vertebral column.
The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve.
An epiphysis that is part of a metacarpal bone of digit 5.
A cruciate ligament in the neck forming part of the atlanto-axial joint. It consists of the transverse ligament of the atlas, along with additional fibers above and below.
A synovial joint that is part of a pelvic girdle region.
A synovial joint that is part of a pectoral girdle region.
in FMA, these are part of the bony pectoral girdle
The humeroulnar joint, is part of the elbow-joint or the Olecron Joint, between the ulna and humerus bones is the simple hinge-joint, which allows for movements of flexion, extension and circumduction. The Humero-Ulnar Joint is the junction of trochlear notch of the ulna and the trochlea of the humerus. Owing to the obliquity of the trochlea of the humerus, this movement does not take place in the antero-posterior plane of the body of the humerus. When the forearm is extended and supinated, the axis of the arm and forearm are not in the same line; the arm forms an obtuse angle with the forearm. During flexion, however, the forearm and the hand tend to approach the middle line of the body, and thus enable the hand to be easily carried to the face. The accurate adaptation of the trochlea of the humerus, with its prominences and depressions, to the semilunar notch of the ulna, prevents any lateral movement. Flexion is produced by the action of the Biceps brachii and Brachialis, assisted by the Brachioradialis, with a tiny contribution from the muscles arising from the medial epicondyle of the humerus. Extension is produced by the Triceps brachii and AnconC&us, with a tiny contribution from the muscles arising from the lateral epicondyle of the humerus, such as the Extensor digitorum communis.
A hinge joint between the head of the radius and the capitulum of the humerus.
A joint that connects the tibia and the fibula.
we include location as part of the logical definition to prevent accidental classification of ankle joints as tibiofibular joints
The inferior tibiofibular articulation (tibiofibular syndesmosis) is formed by the rough, convex surface of the medial side of the lower end of the fibula, and a rough concave surface on the lateral side of the tibia. Below, to the extent of about 4 mm. these surfaces are smooth, and covered with cartilage, which is continuous with that of the ankle-joint. The ligaments are: Anterior ligament of the lateral malleolus, Posterior ligament of the lateral malleolus, Inferior transverse ligament of the tibiofibular syndesmosis, Interosseous ligament
The superior tibiofibular articulation is an arthrodial joint between the lateral condyle of the tibia and the head of the fibula. The contiguous surfaces of the bones present flat, oval facets covered with cartilage and connected together by an articular capsule and by anterior and posterior ligaments. When the term 'tibiofibular articulation' is used without a modifier, it refers to the superior, and not the inferior tibiofibular articulation.
The tarsometatarsal articulations are arthrodial joints in the pes.
The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones.
A skeletal joint that connects a laryngeal cartilage.
The cricoarytenoid articulation (or joint) is a joint connecting the cricoid cartilage and the thyroid cartilage.
The cricoarytenoid articulation (or joint) is a joint connecting the cricoid cartilage and the arytenoid cartilage.
A complex joint in the hind limbs of quadruped mammals such as the sheep, horse or dog. It is the equivalent joint to the human knee. It is often the largest synovial joint in the body.
The xiphisternal joint (or xiphisternal synchondrosis) is a location near the bottom of the sternum, where the body of the sternum and the xiphoid process.
Synovial joint between the bases of adjacent metacarpals. Examples: intermetacarpal joint of right second and third metacarpal bones, intermetacarpal joint of right fourth and fifth metacarpal bones.
The intercarpal articulations (articulations of the carpus) can be subdivided into three sets of articulations: Those of the proximal row of carpal bones, those of the distal row of carpal bones, and those of the two rows with each other.
A joint that connects two adjacent metatarsals
In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
A cartilage element that lies between two successive vertebral centra.
Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO]
ligament that joins successive centra. Important in controlling the stiffness of the vertebral column when it flexes.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints.
Any synovial joint that is part of a (free) limb.
The superficial masseter is a separable part of the masseter muscle, is superficial to all other masseter muscle parts, and attaches to the mandibular angle.[FEED]
Ossicle that is part of the appendicular skeleton.
Examples of appendicular ossicles include the patella and meniscus of the knee joint.
Ossicle that is part of the axial skeleton.
Examples of axial ossicles include the ossified tendons adjacent to the neural spines of the vertebral column.
Subdivision of urinary system which consists of the kidney and the ureters.
A muscle capable of adduction. Adduction is a movement which brings a part of the anatomy closer to the middle sagittal plane of the body. It is opposed to abduction.
A muscle that brings a body part closer to the sagittal plane of the body.[TAO]
we place the TAO class here even though it is a cranial muscle; it is defined functionally
Any of the glands in silk-spinning insects and spiders that secrete a protein liquid that hardens into silk on exposure to air.
A gland found in the larvae of lepidoptera. Each gland is made of three cells: the secretory cell, the reservoir cell and the canal cell.
Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue.
A paired hollow organ in the genito-urinary apparatus of Raja (and probably other skates and rays) whose cavity is fluid filled.
A gill that develops_from a pharyngeal gill precursor.
Anatomical structure consisting of a series of membranes which allow dissolved oxygen from the water to pass into the bloodstream and carbon dioxide to pass out of the bloodstream.[AAO]
The respiratory organ of most aquatic animals that breathe water to obtain oxygen, consisting of a filamentous structure of vascular membranes across which dissolved gases are exchanged. [Free_Online_Dictionary]
Gill slits in the pharyngeal region of the intestine, which are also present in (at least) tunicates and acranians, are taken over to the craniote ancestor.[well established][VHOG]
A muscle whose action is to depress the lower jaw.
Muscle located on ventral side of the head, linking the ventral hyoid arch to the dentary. Innervated by ramus mandibularis V and ramus hyoides VII.[TAO]
Muscle that pulls the hyoid apparatus forward and depresses the lower jaw.[AAO]
Source: Winterbottom, R. 1973. A Descriptive Synonymy of the Striated Muscles of the Teleostei. Proceedings of the Academy of Natural Sciences of Philadelphia, Vol. 125 (1973), pp. 225-317.[TAO]
In amphibians, 'Muscle that pulls the hyoid apparatus forward and depresses the lower jaw.' [AAO:0010655]. 'The protractor hyoideus muscle in teleosts is commonly, albeit mistakenly, referred to as the geniohyoideus muscle, which is involved in the coracomandibularis coupling. According to Edgeworth (1935) and Winterbottom (1974), the protractor hyoideus is composed of a fusion of the intermandibularis posterior and the interhyoideus muscles which resulted in the protractor hyoideus which spans the hyoid and mandible. The intermandibularis spans the mandible while the closely apposed interhyoideus spans the hyoid in other fishes. Furthermore, they concluded that any muscle that is homologous to the geniohyoideus (coracomandibularis coupling) in other lower vertebrates has been lost in teleosts, as well as gars. However, the protractor hyoideus muscle is functionally analogous to the coracomandibularis coupling of other vertebrates and so we use it in our discussion to show the phylogenetically broad roles of these couplings in jaw mechanics.'
Surface structure that extends from the chin covering pharynx and larynx.
Surface structure that is the region between the chin and the isthmus. (from http://www.briancoad.com/Dictionary/introduction.htm).[TAO]
The subarachnoid space associated with the lateral cerebral sulcus (Sylvian fissure); contains the M1 segment of the middle cerebral artery and the origin of lenticulostriate arteries, and proximal parts of the middle cerebral artery
Subdivision of skull that consists of the facial bones.
The cuneiform cartilages of the larynx are two small, elongated pieces of yellow elastic cartilage, placed one on either side, in the aryepiglottic fold, where they give rise to small whitish elevations on the surface of the mucous membrane, just in front of the arytenoid cartilages.
Independent cartilage that may occur dorsal or anterior to the prominentiae apicales dorsales of the arytenoid cartilages.[AAO]
compare with AAO def, 'Independent cartilage that may occur dorsal or anterior to the prominentiae apicales dorsales of the arytenoid cartilages.'
cartilago apicalis seu cartilago Santoriniana
The skull can be divided into two: the neurocranium and the facial skeleton
primary subdivision of cranial skeletal system
A suture joining a nasal bone to another bone.
The cartilaginous junction between the basisphenoid and basioccipital bones of the mammalian skull
in humans, usually closed by the age of 25
A cartilaginous condensation that has_potential_to_develop_into a supraoccipital bone.
non-squamous part of supraoccipital bone
A pre-cartilage condensation that has_potential_to_develop_into a supraoccipital bone.
supra-occipital pre-cartilage condensation
supraoccipital pre-cartilage condensation
A bone that is part of a neurocranium [Automatically generated definition].
Longitudinal fibers of the esophagus that attaches to the posterior aspect of the cricoid cartilage of the larynx
Paired, intramembranous bones located within the nasal capsules and embedded in the nasal cartilages; it is pierced by the ductus nasolacrimalis.
A small dermal bone of the facial series that is often absent; when present it is usually sunken beneath the surface bones and aids in forming the nasal cavity
A bone behind and above the orbit of which it commonly forms part of the border that is present in many vertebrates and corresponds to the postorbital process of the frontal bone of various birds and mammals
The postorbital is one of the bones in vertebrate skulls which forms a portion of the dermal skull roof and, sometimes, a ring about the orbit. Generally, it is located behind the postfrontal and posteriorly to the orbital fenestra. In some vertebrates, the postorbital is fused with the postfrontal to create a postorbitofrontal.
A skeletal joint that connects quadrate and articular bones.
over time, the synapsids' quadrate-articular jaw joint (which the rest of the tetrapods possess) was replaced by a dentary-squamosal joint (which all living mammals possess), while the quadrate and articular migrated, shrank, and became part of the complex of middle ear bones.
see comments for UBERON:0004744 articular/anguloarticular.
Joint that articulates quadrate and anguloarticular bones. Quadrate-articular joint is paired.[TAO]
Skeletal joint that articulates bones of upper and lower jaw.
Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
The term retrorubral area of the midbrain reticular nucleus refers to a region of the rat brain caudal and dorsal to the ventral tegmental area. It is one of three parts of the midbrain reticular nucleus; the other two are the magnocellular part of the midbrain reticular nucleus and the parvicellular part of the midbrain reticular nucleus (Swanson-2004). BrainInfo distinguishes between the Retrorubral area of the midbrain reticular formation and the retrorubral nucleus.
midbrain reticular nucleus, retrorubral area
midbraiin reticular nucleus, retrorubral area
The term anterior nuclei of stria terminalis refers to one of two divisions of the nuclei of stria terminalis based on topology, connectivity and multiple stains in the rat ( Swanson-2004 ) and the mouse ( Dong-2004 ). The other division consists of the posterior nuclei of stria terminalis. The anterior division includes the anterolateral area of stria terminalis, anteromedial area of stria terminalis, oval nucleus of stria terminalis, juxtacapsular nucleus of stria terminalis, rhomboid nucleus of stria terminalis, dorsomedial nucleus of stria terminalis, fusiform nucleus of stria terminalis, ventral nucleus of stria terminalis, and the magnocellular nucleus of stria terminalis
bed nuclei of the stria terminalis, anterior division
anterior part of the bed nucleus of the stria terminalis
bed nuclei of the stria terminalis anterior division
bed nuclei of the stria terminals anterior division
bed nucleus of the stria terminalis anterior division
bed nucleus of the stria terminalis anterior part
bed nucleus of thestria terminalis anterior division
anterior division of bed nuclei of stria terminalis
bed nuclei of the stria terminalis, anterior division, fusiform nucleus
bed nuclei of the stria terminalis anterior division fusiform nucleus
bed nuclei of the stria terminalis fusiform nucleus
bed nuclei of the stria terminals anterior division fusiform nucleus
bed nucleus of the stria terminalis fusiform nucleus
bed nucleus of the stria terminalis fusiform part
bed nuclei of the stria terminalis, anterior division, oval nucleus
The term posterior nuclei of stria terminalis refers to one of two divisions of the nuclei of stria terminalis based on topology, connectivity and multiple stains in the rat ( Swanson-2004 ) and the mouse ( Dong-2004 ). The other division consists of the anterior nuclei of stria terminalis. The posterior division includes the principal nucleus of stria terminalis, interfascicular nucleus of stria terminalis, transverse nucleus of stria terminalis, premedullary nucleus of stria terminalis, dorsal nucleus of stria terminalis, the strial extension of stria terminalis, and the cell sparse zone of stria terminalis.
bed nuclei of the stria terminalis, posterior division
bed nuclei of the stria terminalis posterior division
bed nucleus of stria terminalis posterior part
bed nucleus of the stria terminalis posterior division
posterior part of the bed nucleus of the stria terminalis
posterior division of bed nuclei of stria terminalis
bed nuclei of the stria terminalis, posterior division, principal nucleus
bed nuclei of the stria terminalis posterior division principal nucleus
bed nuclei of the stria terminalis principal nucleus
bed nucleus of the stria terminalis principal (encapsulated) nucleus
bed nuclei of the stria terminalis, posterior division, transverse nucleus
bed nuclei of the stria terminalis posterior division transverse nucleus
bed nuclei of the stria terminalis transverse nucleus
bed nucleus of the stria terminalis transverse nucleus
Corpus spongiosum (also known as corpus cavernosum urethrae in older texts) is the mass of spongy tissue surrounding the male urethra within the penis.
The function of the corpus spongiosum in erection is to prevent the urethra from pinching closed, thereby maintaining the urethra as a viable channel for ejaculation. To do this, the corpus spongiosum remains pliable during erection while the corpora cavernosum penis becomes engorged with blood.
An epithelium that is part of a crypt of Lieberkuhn.
FMA has classes for subdivisions of this epithelium
A sphincter muscle that is part of the gastrointestinal system
small, mucous accessory lacrimal glands that are found underneath the eyelid where the upper and lower conjuctivae meet. Their ducts unite into a rather long sinus which open into the fornix conjunctiva. There are approximately forty Krause glands in the region of the upper eyelid, and around 6 to 8 in the region of the lower lid. The function of these glands are to produce tears which are secreted onto the surface of the conjuctiva
The greater tubercle of the humerus is situated lateral to the head of the humerus and posteriolateral to the lesser tubercle. Its upper surface is rounded and marked by three flat impressions. the highest of these gives ('superior facet') insertion to the Supraspinatus the middle ('middle facet') to the Infraspinatus. the lowest one ('inferior facet'), and the body of the bone for about 2.5 cm. below it, to the Teres minor. The lateral surface of the greater tubercle is convex, rough, and continuous with the lateral surface of the body. Between the greater tubercle and the lesser tubercle is the intertubercular sulcus (bicipital groove).
The lesser tubercle of the humerus, although smaller, is more prominent than the greater tubercle: it is situated in front, and is directed medially and anteriorly. Above and in front it presents an impression for the insertion of the tendon of the Subscapularis.
A lamina propria that is part of a large intestine.
lamina propria of mucosa of large intestine
A crescent-shaped whitish area of the bed of a fingernail or toenail. The lunula is the visible part of the nail matrix (i.e. the root of the nail).
Ophthalmic veins are veins which drain the eye. More specifically, they can refer to: Superior ophthalmic vein Inferior ophthalmic vein
The superior ophthalmic vein begins at the inner angle of the orbit in a vein named the nasofrontal which communicates anteriorly with the angular vein; it pursues the same course as the ophthalmic artery, and receives tributaries corresponding to the branches of that vessel. Forming a short single trunk, it passes between the two heads of the Rectus lateralis and through the medial part of the superior orbital fissure, and ends in the cavernous sinus. The ethmoidal veins drain into the superior ophthalmic vein. Vorticose veins also drain into the superior ophthalmic vein.
The inferior ophthalmic vein begins in a venous net-work at the forepart of the floor and medial wall of the orbit; it receives some vorticose veins and other veins from the Rectus inferior, Obliquus inferior, lacrimal sac and eyelids, runs backward in the lower part of the orbit and divides into two branches. One of these passes through the inferior orbital fissure and joins the pterygoid venous plexus, while the other enters the cranium through the superior orbital fissure and ends in the cavernous sinus, either by a separate opening, or more frequently in common with the superior ophthalmic vein.
An autonomic plexus, entering the orbit in company with the ophthalmic artery, derived from the internal carotid plexus.
An epithelium that is part of a inferior parathyroid gland.
An epithelium that is part of a superior parathyroid gland.
An epithelium that is part of a parathyroid gland.
A muscle layer that is part of a large intestine.
A small indentation located in the prostatic urethra, at the apex of the urethral crest, on the seminal colliculus (verumontanum), laterally flanked by openings of the ejaculatory ducts. It is also known as the vagina masculina or (in older literature) vesicula prostatica. It is often described as 'blind,' meaning that it is a duct that does not lead to any other structures. It can sometimes be enlarged.
add df relations. Check mesopnephric duct
The sacrococcygeal symphysis (sacrococcygeal articulation, articulation of the sacrum and coccyx) is an amphiarthrodial joint, formed between the oval surface at the apex of the sacrum, and the base of the coccyx. It is a slightly moveable joint which is frequently, partially or completely, obliterated in old age, homologous with the joints between the bodies of the vertebrae.
A muscle layer that is part of a small intestine.
An epithelium that is part of a urachus.
Mesenchyme that is part of a developing urachus.
Between the rectum and the bladder the peritoneal cavity forms, in the male, a pouch, the rectovesical excavation (or rectovesical pouch), the bottom of which is slightly below the level of the upper ends of the vesiculae seminalesbi. e. , about 7.5 cm. from the orifice of the anus. its lowest part membranous partition called Rectoprostatic fascia. The corresponding structure in women is the rectouterine pouch.
The carpometacarpus is the fusion of the carpal and metacarpal bone, essentially a single fused bone between the wrist and the knuckles. It is a smallish bone in most birds, generally flattened and with a large hole in the middle. In flightless birds, however, its shape may be slightly different, or it might be absent entirely.
A joint that allows motion around an axis.
The iliocostalis lumborum (iliocostalis muscle; sacrolumbalis muscle) is inserted, by six or seven flattened tendons, into the inferior borders of the angles of the lower six or seven ribs.
medial migration pathway NC-derived mesenchyme
lateral migration pathway NC-derived mesenchyme
A root of cranial nerve that is part of a vagus nerve.
FMA distinguishes between roots and rootlets - we mix the two here
A neural nucleus that is part of a midbrain tectum.
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
Anatomical structure, which consists of a specific set of the members of (predominantly) one organ or organ part subclass interconnected by zones of continuity or body substances; is demarcated from other subdivisions of the same organ system by one or more zones of continuity or anatomical lines; together with other subdivisions of the same organ system, it constitutes an organ system. Examples: rib cage, facial skeleton, portal system, central nervous system, upper respiratory tract, muscle group of back.
Origin: spinous processes of seventh cervical and sometimes two upper thoracic vertebrae; insertion: spinous processes of axis and sometimes of second to fourth cervical vertebrae; innervation: branches of cervical; action: extends vertebral column.
The Spinalis cervicis (Spinalis colli) is an inconstant muscle, which arises from the lower part of the ligamentum nuchæ, the spinous process of the seventh cervical, and sometimes from the spinous processes of the first and second thoracic vertebrae, and is inserted into the spinosus process of the axis, and occasionally into the spinous processes of the two vertebrae below it. [Wikipedia:Spinalis#Spinalis_cervivis]
Lumbar muscle that extends and rotates the vertebral column.
The mastoid process is a conical prominence projecting from the undersurface of the mastoid portion of the temporal bone. It is located just behind the external acoustic meatus, and lateral to the styloid process. Its size and form vary somewhat; it is larger in the male than in the female. This process serves for the attachment of the posterior belly of the digastric, sternocleidomastoid, splenius capitis, and longissimus capitis muscles. The word is derived from the Greek 'masto-', alluding to its resemblance to the breast.
The ora serrata is the serrated junction between the retina and the ciliary body. This junction marks the transition from the simple non-photosensitive area of the retina to the complex, multi-layered photosensitive region. In animals in which the region does not have a serrated appearance, it is called the ora ciliaris retinae.
Muscles within the eye (bulbus oculi).[AAO]
Synovial sac which surrounds parts of one or more tendons . Examples: synovial tendon sheath of manual digit 2, radial bursa.
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
fibrous membrane of synovial tendon sheath
Deep fascia (or 'investing fascia') is a layer of fascia which can surround individual muscles, and divide groups of muscles into compartments. This is the dense fibrous connective tissue that interpenetrates and surrounds the muscles, bones, nerves and blood vessels of the body. It provides connection and communication in the form of aponeuroses, ligaments, tendons, retinacula, joint capsules, and septa. The deep fasciae envelop all bone; cartilage, and blood vessels and become specialized in muscles and nerves. The high density of collagen fibers is what gives the deep fascia its strength and integrity. The amount of elastin fiber determines how much extensibility and resilience it will have.
FMA considers parietal fascia a different class
Visceral fascia suspends the organs within their cavities and wraps them in layers of connective tissue membranes. Each of the organs is covered in a double layer of fascia; these layers are separated by a thin serous membrane. The outermost wall of the organ is known as the parietal layer The skin of the organ is known as the visceral layer. The organs have specialized names for their visceral fasciae. In the brain, they are known as meninges; in the heart they are known as pericardia; in the lungs, they are known as pleura; and in the abdomen, they are known as peritonea. [Wikipedia:Visceral_fascia]
Endochondral bone that extends forward from the frontal bones and articulates posterolaterally with the lateral ethmoids and the vomer and parasphenoid ventrally. The mesethmoid is an unpaired bone[TAO:0000323].
The most anterior region of the braincase. Provides structural support for peripheral olfactory organ.
currently this is not restricted to skeletal elements, unlike UBERONREF:0000007
Region between capsules formed by anterior tips of neurocranial trabeculae.
Chondrocranium cartilage that is initially plate-like and formed from the anterior fusion of the trabecula crani. The ethmoid cartilage is paired.[TAO]
We assume the AAO structure is cartilage
The perpendicular plate of the ethmoid bone (vertical plate) is a thin, flattened lamina, polygonal in form, which descends from the under surface of the cribriform plate, and assists in forming the septum of the nose; it is generally deflected a little to one or other side. The anterior border articulates with the spine of the frontal bone and the crest of the nasal bones. The posterior border articulates by its upper half with the sphenoidal crest, by its lower with the vomer. The inferior border is thicker than the posterior, and serves for the attachment of the septal cartilage of the nose. The surfaces of the plate are smooth, except above, where numerous grooves and canals are seen; these lead from the medial foramina on the cribriform plate and lodge filaments of the olfactory nerves.
lamina perpendicularis ossis ethmoidalis
One of the canals of the orbital surface of the maxilla, the infraorbital canal, opens just below the margin of the orbit.
VSAO sais that the procoracoid+coracoid are homologous to the teleost coracoid. Consider adding a separate class for posterior coracoid.
Kardong states that the procoracoid (or the anterior part of the procoracoid) is homologous to the coracoid, but this is controversial
In primitive synapsis 3 centers develop in the shoulder: the dorsal center gives rise to the scapula and the two ventral centers produce an anterior coracoid (procoracoid) and posterior coracoid (coracoid)
Cartilaginous, paired structures located on the anterolateral portions of the zonal area of the pectoral girdle.[AAO]
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.
A skeletal muscle in the posterior triangle of the neck. It originates on the transverse processes of the upper cervical vertebrae and is inserted in the lateral half of the clavicle
Cleidocervicalis is one of two muscles, which make up the cleidocephalic component of the complex brachiocephalic muscle. It is a thin triangular muscle which has a broad origin on the median raphe of the mid dorsal aspect of the neck. The muscle is bounded caudally by the trapezius and cranially by the occipital component of the sternocephalicus . The cleidocervicalis tapers as it passes ventrally across the side of the neck to insert into the clavicular tendon. It is innervated by the accessory nerve. The brachiocephalic complex advances the limb, extends the shoulder joint and fixes the neck.
The levator claviculae is an infrequently recognized anatomical variant in humans, distinguished from, for example, cervical adenopathy or a thrombosed vein, but a normal muscle in lower mammals and anthropoids. In humans, when present, it often appears unilaterally, most commonly on the left side, or bilaterally.
Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal—not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals.
Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820].
A sensory organ in which the epidermis is modified to form bulbous papillae. The organs are formed from a stack of epidermal cells, which is innervated by nerve processes from myelinated fibers in the dermis, which form terminal swellings just below the outer keratinized layer of epidermis. They contain a Merkel cell-neurite complex in the epidermis and a lamellated corpuscle in the dermal connective tissue.
present in many moles, and are particularly common in the star-nosed mole, which bears 30,000 of them on its unique tentacled snout
Moist, hairless, crenelated area around nostrils of some mammals
A gland arranged along a row on the underside of the hindlimb in some lizards[Kardong]
Femoral pores are a part of a holocrine secretory gland found on the inside of the thighs of certain lizards and amphisbaenians which releases pheromones to attract mates or mark territory. In certain species only the male has these pores and in other species, both sexes have them, with the males being larger.[1] Femoral pores appear as a series of pits or holes within a row of scales on the ventral portion of the animal's thigh.
Femoral pores are present in all genera in the families Cordylidae, Crotaphytidae, Hoplocercidae, Iguanidae, Phrynosomatidae, and Xantusiidae. They are absent in all genera in the Anguidae, Chamaeleonidae, Dibamidae, Helodermatidae, Scincidae, Xenosauridae, and Varanidae families.[1] They are present in other lizards and amphisbaenians quite variably, some geckoes, Phelsuma, for example have these pores, others in the same family do not
A carpometacarpal joint that connects to metacarpal 1.
In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average
Made obsolete as the ear muscle inserts into cartilage and aponeurosis without any intervening tendon
The quadratojugal is a small jaw bone that is present in most amphibians, reptiles, and birds, but has been lost in mammals. It is connected to the jugal as well as other bones, though these may vary with species. The quadratojugal bone is a small bone between the cheek and otic notch (Lecointre 380). Squamates (lizards and snakes) lack a quadratojugal bone (Schwenk 193).
Paired intramembranous bones that completes the maxillary arch posteriorly; they appear at the end of, or just after, metamorphosis[AAO:0000532].
A secondary tongue located below the primary tongue in prosimian primates and some primitive mammals. This structure does not have taste buds or salivary glands
The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA].
Subdivision of vertebral column that is posterior to the sacral region and anterior to the caudal region.
Definition to be reviewed for generality across tetrapods. Typically we regard the caudal region as immediately following the sacral region, with the caudal (tail) region defined as post-anal.
Region of the vertebral column posterior to the sacrum consisting of two to four vertebrae. The last of these vertebrae is distinguished by the possession of a well-developed haemal arch; it supports the posterior part of the cloaca and marks the posterior limit of the trunk.[AAO]
caudal-sacral region of vertebral column
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
A nail that is part of a manual digit 1.
A nail that is part of a manual digit 2.
A nail that is part of a manual digit 3.
A nail that is part of a manual digit 4.
A nail that is part of a manual digit 5.
A remnant of the Mesonephric duct that can be found next to the ovary and fallopian tube.
A putative electroreceptor organ located in the medial rostral cavity in the ethmoid portion of the chondrocranium of Coelacanths. It is surrounded by an insulating layer of adipose tissue and innervated by the superficial ophthalmic nerve.
classification as electric organ is putative
A flexible, unpaired, hollow tube found in hemichordates that arises in embryonic development as an outpocketing from the roof of the embryonic gut anterior to the pharynx. In adults, they extend dorsally from the pharynx into the probiscis, and serve to communicate with the oral cavity.
Their walls are composed primarily of epithelial cells, but ciliated and glandular cells are also present.
The pharyngeal aponeurosis (or pharyngobasilar fascia, or fibrous coat), is situated between the mucous and muscular layers. It is thick above where the muscular fibers are wanting, and is firmly connected to the basilar portion of the occipital and the petrous portions of the temporal bones. As it descends it diminishes in thickness, and is gradually lost. It is strengthened posteriorly by a strong fibrous band, which is attached above to the pharyngeal spine on the under surface of the basilar portion of the occipital bone, and passes downward, forming a median raphe, which gives attachment to the Constrictores pharyngis.
The submucous layer of the wall of the uterine tube.
A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum.
CNS white matter that is part of the telencephalon[ZFA:0000597].
predominantly white regional part of telencephalon
A portion of gray matter that is part of a telencephalon.
predominantly gray regional part of telencephalon
manubrium sterni pre-cartilage condensation
manubrium sternum pre-cartilage condensation
Outer covering of an animal typically consisting primarily of cellulose (tunicin) in addition to varying amounts of water, protein and carbohydrates. The tunicate is a characteristic feature of Tunicata
In some species tunicin occurs in small amounts. Some species calcium salts are deposited as spicules. In ascidians, the tunic is supplied with blood vessels.
Basalmost subdivision of a tunicate containing the heart and reproductive organs
The superficial temporalis muscle is a separable part of the temporalis muscle that attaches to the temporalis fascia.[FEED]
The deep temporalis muscle is a separable part of the temporalis muscle that that attaches to the bony wall of the braincase and is deep to the superficial temporalis.[FEED]
The suprazygomatic part of the temporalis muscle is a separable part of the deep temporalis that attaches to the superior surface of the temporal root of the zygomatic arch.[FEED]
The pars reflexa is a separable part of the superficial masseter muscle that attaches to the medial surface of the mandible.
The pars reflexa is a separable part of the superficial masseter muscle that attaches to the medial surface of the mandible.[FEED]
The body of the mandible is curved somewhat like a horseshoe and has two surfaces and two borders.
.The fossa for the masseter. In some therapsids, the coronoid process of the dentary bears a large external depression which accommodates the masseter -- an important muscle in closing and in grinding motions of the jaw.
fossa on the lateral surface of the mandible, located in the superior part of the ascending process.[FEED]
An elastic band connecting the anterior surface of the epiglottis to the upper border of the body of the hyoid bone.
Developed in mammals other than human. EDITOR NOTE: TODO add relationship to hyoepiglottic ligament.
The posterior masseter is a separable part of the deep masseter muscle that attaches to the postero-ventral surface of the zygomatic arch.[FEED]
The anterior masseter is a separable part of the masseter muscle that is attached to anterior root of zygomatic arch.[FEED]
The digastric branch of facial nerve arises close to the stylomastoid foramen, and divides into several filaments, which supply the posterior belly of the Digastricus; one of these filaments joins the glossopharyngeal nerve.
digastric branch of facial nerve (CN VII)
branch of facial nerve to posterior belly of digastric
The stylohyoid branch of facial nerve frequently arises in conjunction with the digastric branch; it is long and slender, and enters the Stylohyoideus about its middle.
branch of glossopharyngeal nerve to stylopharyngeus
ramus musculi stylopharyngei nervus glossopharyngei
stylopharyngeal branch of glossopharyngeal nerve
nerve to stylopharyngeus from glossopharyngeal nerve
The articular capsule (capsular ligament) is a thin, loose envelope, attached above to the circumference of the mandibular fossa and the articular tubercle immediately in front; below, to the neck of the condyle of the mandible.
articular capsule of temporomandibular joint
capsula articularis articulationis temporomandibularis
The fibrocartilaginous plate that separates the joint into upper and lower cavities.
articular disc of temporomandibular joint
articular disk of temporomandibular joint
discus articularis (articulatio temporomandibularis)
discus articularis articulationis temporomandibularis
The masseteric nerve passes laterally, above the Pterygoideus externus, in front of the temporomandibular articulation, and behind the tendon of the Temporalis; it crosses the mandibular notch with the masseteric artery, to the deep surface of the Masseter, in which it ramifies nearly as far as its anterior border. It gives a filament to the temporomandibular joint.
A nerve that innervates the mylohyoid muscle and the anterior belly of the digastric muscle.
branch of inferior alveolar nerve to mylohyoid
mylohyoid branch of inferior alveolar nerve
The pharyngeal plexus is a network of nerve fibers innervating most of the palate, larynx, and pharynx. It is located on the surface of the middle pharyngeal constrictor muscle.
The superior laryngeal nerve is a branch of the vagus nerve. It arises from the middle of the ganglion nodosum and in its course receives a branch from the superior cervical ganglion of the sympathetic. It descends, by the side of the pharynx, behind the internal carotid artery, and divides into two branches: external laryngeal nerve internal laryngeal nerve A superior laryngeal nerve palsy changes the pitch of the voice and causes an inability to make explosive sounds. If no recovery is evident three months after the palsy initially presents, the damage is most likely to be permanent. A bilateral palsy presents as a tiring and hoarse voice.
superior laryngeal branch of inferior vagal ganglion
The deep temporal nerves, branches of the mandibular division of the trigeminal nerve, are two in number, anterior and posterior. They pass above the upper border of the pterygoideus externus and enter the deep surface of the temporalis.
A anatomical surface that is part of a mandible.
The Pharyngeal raphe is a raphe that serves as the origin and insertion for several of the pharyngeal constrictors.
A raphe running across the palate, from the palatine uvula to the incisive papilla.
A palatine raphe that is part of a hard palate.
A palatine raphe that is part of a soft palate.
The pterygomandibular raphe (pterygomandibular ligament) is a tendinous band of the buccopharyngeal fascia, attached by one extremity to the hamulus of the medial pterygoid plate, and by the other to the posterior end of the mylohyoid line of the mandible. Its medial surface is covered by the mucous membrane of the mouth. Its lateral surface is separated from the ramus of the mandible by a quantity of adipose tissue. Its posterior border gives attachment to the superior pharyngeal constrictor muscle. Its anterior border attaches to the posterior edge of the buccinator.
An acellular strand that runs from subcommissural organ caudally through the ventricular system and central canal to the ampulla caudalis. Develops from glycoproteins secreted into CSF.
Reissner's fiber is present in the central canal of species in all chordate subphyla[Olsson R. (1993) Reissner's fiber mechanisms: some common denominators. In The Subcommissural Organ: An Ependymal Brain Gland ]
Resembles the subcommisural organ structurally, ultrastructurally and immunochemically[Niewenhuys] Gives rise to Reissner's fiber; however secretions are not identical to those of SCO [PMID:9550137][doi:10.1007/BF00303086]
This is a neurosecretory organ rostral to the ampulla caudalis on the ventral surface of the distal end of the spinal cord. Receives axons from caudal neurosecretory nucleus, which contains Dahlgren cells that secrete urotensin I and II, implicated in osmotic regulation, cardiovascular function and reproduction[Butler].
Shares characteristics with neurohypophysis
A ventricle-like space at the end of the central canal
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
A lymph vasculature that is part of a head.
The cleidomastoideus is a thick, strap-like muscle that together with the cleidocervicalis forms the proximal part of the brachiocephalicus. It lies beneath the cleidocervicalis. Its origin is the clavicular tendon with its insertion being at the mastoid process of the temporal bone. It is distinctly narrow and is united with the cleidocervicalis and cleidobrachialis by the clavicular tendon. Together with the other two components of the brachiocephalicus muscle, its primary function is to advance the free limb, however, it can also act as an shoulder extensor. Acting bilaterally, it fixes and depresses the neck, while by its unilateral action, it allows the head and neck to be drawn to the side. Its blood supply is the inferior cervical, carotid and vertebral arteries and its nerve supply is the spinal accessory, cervical and axillary nerves.
alt def: "Combination of cleidomastoid and cleidocervical muscles"
This muscle makes up the distal segment of the brachiocephalicus. It originates at the clavicular tendon but functionally, from the head and neck through the cleidocervicalis. It inserts at the distal end of the cranial border of the humerus, where it lies between the biceps brachii medially and the brachialis laterally. The muscle partly covers the pectoral muscles at their insertions. In conjunction with the cleidocervicalis, it advances the limb, extends the shoulder and causes lateral movement of the head and neck.
The brachiocephalicus is a long and flat, complex of muscles that extends from the lower half of the humeral shaft to the head and neck. The muscle divides into two parts at the clavicular intersection. This is also the point of origin for all the muscles that make up the brachiocephalicus. This point is situated just cranial to the shoulder. The two main sections are the cleidobrachialis which is distal to the clavicular intersection and the cleidocephalicus which extends proximally to the clavivular intersection. The cleidocephalicus can also be divided into the pars cervicalis, which inserts on the broad aponeurosis, over the fibrous raphe of the cranial half of the neck. The other part, the pars mastoideus inserts on the mastoid process of the temporal bone via a strong tendon. The cleidobrachialis extends distally from the clavicular intersection and inserts on the cranial edge of the distal half of the humerus. The tendon that inserts the cleidobrachialis lies between the brachialis muscle and the biceps brachii. As a result of the brachiocephalicus spanning a large region it has the ability to provide a number of actions. These include extending the shoulder joint, protracts the limb, provides lateral movement of the head and allows the neck to be depressed.
The brachiocephalicus is more complex than other muscles of the forelimb. It consists of 2 elements that unite at the clavicle in dogs. In dogs the caudal part, known as the cleidobrachialis, runs from the clavicle to the humerus and is closely associated with the deltoid. The cranial portion runs from the clavicle to various attachments via a broad aponeurosis on the upper part of the head and neck. It is called the cleidomastoideus in the dog because it inserts on the mastoid process of the temporal bone. It may have a different name, like cleido-occipitalis, in other mammals. The name brachiocephalicus signifies that this complex of muscles runs from the upper arm to the head and does not specify the details of muscle attachments because these vary so much from species to species. The brachiocephalicus advances the limb and may also extend the shoulder joint, but this depends on the cranial attachment being fixed and the limb being free to move. However, when the forelimb is firmly on the ground and the head is free to move, it forces the head and neck either ventrally or to one side depending on whether or not both muscles act in tandem
The omotransversarius is a straplike muscle, which advances and adducts the forelimb, as well as flexes the neck laterally. It covers the transverse processes of the cervical vertebrae, lying to their side. The omotransversarius lies ventral to the trapezius, cranial to the deltoid muscle and is covered cranially by the cleidocervicalis. It extends from the atlas to the spine of the scapula, with its origin on the transverse process of the atlas and its insertion in the distal end of the spine of the scapula. Its name can be split into omo, which is Greek for shoulder, and tranversarius which relates to its attachment to the transverse process of the atlas. This muscle is innervated by the accessory nerve.
A transverse process of vertebra that is part of a vertebral bone 1.
The sternocephalicus is a flat muscle and its caudal border is adjacent to the ventral border of the brachiocephalicus. The lateral aspect of this muscle is crossed obliquely by the external jugular vein. It originates as a unit on the first sternebrae. The cranial portion of the muscle divides into two separate sections with different insertion points. These are the sternomastoideus and the sterno-occipitalis. The ventral portion, the sternomastiodeus is the stronger and main continuation of the sternocephalicus, which inserts on the mastoid part of the temporal bone. The thin but wide dorsal segment, the sterno-occipitalis attaches to the dorsal nuchal crest by a thin aponeurosis. The main action provided by the sternocephalicus is movement of the head and neck to the side. Ventral branches of the cervical nerves are attached to this muscle.
this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue
A zone of skin that is part of a prepuce of clitoris.
The iliothoracic group is made up of the abdominal wall muscles: rectus abdominis, external abdominal oblique, internal abdominal obliquus, and the transversus abdominis
The femorospinal group is made up of the psoas major and iliacus muscles
The external sphincter muscle of urethra (or sphincter urethrae membranaceae) surrounds the whole length of the membranous portion of the urethra, and is enclosed in the fasciæ of the urogenital diaphragm. They arch across the front of the urethra and bulbourethral glands, pass around the urethra, and behind it unite with the muscle of the opposite side, by means of a tendinous raphé.
MA includes a term bulboglandular - some sources claim this as the muscles that are associated with the bulbourethral gland, so we place this here
external urethral sphincter of male urethra
musculus sphincter urethrae externus urethrae masculinae
The external sphincter muscle of female urethra is a muscle which controls urination.
external urethral sphincter of female urethra
musculus sphincter urethrae externus urethrae femininae
A blood vessel running parallel to the inferior pancreatico-duodenal artery that drains blood from the pancreas and duodenum into the splenic vein.
Is one of the numerus muscles of the external ear and is of importance since it is encountered in the operation for drainage of infections of the external ear of the dog. As its name suggests, it arises from the fascia over the parotid gland and approaches the auricle from the ventrolateral direction. This muscle is supplied by the facial nerve.The muscles of the external ear with their scattered origins and precisely located insertions provide for displacement and rotation of the ear in all directions. These muscles also have a collective function in communication both within and between species.
A chiasma of facial muscles held together by fibrous tissue, located lateral and slightly superior to each angle of the mouth. It is important in moving the mouth, facial expression and in dentistry. It derives its motor nerve supply from the facial nerve, and its blood supply from labial branches of the facial artery. It is contributed to by the following muscles: orbicularis oris, buccinator, levator anguli oris, depressor anguli oris, zygomaticus major, risorius quadratus labii superioris, quadratus labii inferioris.
The constrictor muscle of the labia is weakly developed in the female dog which blends dorsally with the external anal sphincter muscle and attaches to the coccygeal fascia at the level of the first and second coccygeal vertebrae. It encircles the vulva and vestibule for a distance of about 1 cm. caudal to the area where the urethra enters the vestibule. Its action is to lift the labia dorsally to facilitate intromission of the penis into the vagina. The constrictor vestibuli and vulvae are homologous to the bulbospogiosus (bulbocavernosus) muscle in the male.
A bulbospongiosus muscle that is part of a male reproductive system.
The bulbospongiosus is the thick extrapelvic continuation of the urethralis. It originates from the perineal body (and midline raphe over corpus spongiosum in male) and inserts at the superficial perineal membrane and dorsal penile or clitoral aponeurosis. In males, the bulbospongiosus muscles are united and surround the base of the penis. They aid in emptying of urine and ejaculate from urethra. In females, these muscles are separated in the middle by the vagina and act to constrict the vaginal introitus. They can also stop the flow of blood into veins, which maintains an erection in the penis of the male and the clitoris of the female. Its nerve connection is the perineal branch of the pudendal nerve (S2, 3, 4).
The pudendal nerve is a somatic nerve in the pelvic region that innervates the external genitalia of both sexes, as well as sphincters for the bladder and the rectum. It originates in Onuf's nucleus in the sacral region of the spinal cord.
A nerve arising from the pudendal nerve that supplies the perineum.
A layer of elastic tissue that forms the outermost part of the tunica intima of blood vessels.
Lying just below the skin, cutaneus trunci is one of very few cutaneus muscles. It composes of a thin sheets of muscle that spred over the body in the superficial fasciae. Their role is to twich the skin to rid of pests etc. Cuteneus muscles are found in all domestic species.
covers the entire body with a thin layer of muscle under the deepest layer of the skin. When an area of neuronal subluxation is stimulated with the activator, the cutaneous trunci muscle contracts and causes an involuntary reflexive spasm or "twitch" of the skin
Is a principal muscle of the lips which arises over the dorsum of the nose. It runs cranioventrally to insert partly on the wing of the nostril and partly into the lateral part of the upper lip. This muscles function includes dilation of the nostril, elevation and retraction of the upper lip. Branches of the facial nerve supply innervation to this muscle.
A muscle that runs beneath the longissimus capitis and inserts on the wing of the atlas
The ventral lateral sacrocaudal is a long strong muscle consisting of numerous individual parts. Its first segment originates from the last lumbar vertebrae and the remainder from the transverse processes of the caudal vertebrae. From the segmented bellies arise long tendons which are embedded in caudal fascia. The first of these tendons inserts onto the sixth caudal vertebrae, the second onto the seventh and so on until the last caudal vertebrae. The ventral lateral sacrocaudal acts to flex the tail and occasionally assists with lateral movement.
Rectus thoracis is a very small quadrilateral muscle sheet from the lateral thorax runs from the 3rd-1st rib that is in continuation with rectus abdominis. Its functioning muscle in respiration.
The sphincter colli superficialis is composed of transverse muscle fibers, and covers the entire area between the lower jaw and chest. The muscle is used to tighten the skin on the underside of the throat.
M. sphincter colli superficialis is present in Lagomorpha but absent in Rodentia (Meinertz, 1941, 1942; Ryan, 1989; Rinker, 1954). Some errouneous references of this muscle in rodents (e.g., Bezuidenhout and Evans, 2005) are due to decussating fibers of the deep sphincter, which creates a false superficial sphincter (Ryan, 1989)
The sphincter colli profundus lies below the platysma in the area of the parotid gland (gland regions).
The muscles of the mid and upper face derive from the embryonic sphincter colli profundus muscle
The Iliococcygeus arises from the ischial spine and from the posterior part of the tendinous arch of the obturator fascia, and is attached to the coccyx and anococcygeal raphC); it is usually thin, and may fail entirely, or be largely replaced by fibrous tissue. It is part of the levator ani group of muscles. An accessory slip at its posterior part is sometimes named the Iliosacralis.
The fibers which form a sling for the rectum are named the Puborectalis or Sphincter recti. They arise from the lower part of the symphysis pubis, and from the superior fascia of the urogenital diaphragm. They meet with the corresponding fibers of the opposite side around the lower part of the rectum, and form for it a strong sling. Relaxation reduces the angle between rectum and anus, allowing defecation in conjunction with relaxation of the internal and external sphincters. Puborectalis is part of the levator ani group of muscles.
The pubococcygeus muscle or PC muscle is a hammock-like muscle, found in both sexes, that stretches from the pubic bone to the coccyx (tail bone) forming the floor of the pelvic cavity and supporting the pelvic organs. It is part of the levator ani group of muscles.
A pubococcygeus muscle that is part of a male organism.
Pubovaginalis in the female is the equivalent of levator prostatae in the male.
Originates on the distal radioulna and inserts on the palmar prepollex.
The Chondroglossus is sometimes described as a part of the Hyoglossus, but is separated from it by fibers of the Genioglossus, which pass to the side of the pharynx. It is about 2 cm. long, and arises from the medial side and base of the lesser cornu and contiguous portion of the body of the hyoid bone, and passes directly upward to blend with the intrinsic muscular fibers of the tongue, between the Hyoglossus and Genioglossus.
Originates from the distal carpal 5-4-3 and inserts on the palmar prepollex.
An anatomical cavity that is part of a esophagus.
A tube lumen that is part of a mesonephric duct.
The styloid process of the ulna projects from the medial and back part of the bone; it descends a little lower than the head, and its rounded end affords attachment to the ulnar collateral ligament of the wrist[WP,unvetted].
A bony ridge located above the eye sockets of all primates. In Homo sapiens sapiens (modern humans) the eyebrows are located on their lower margin[WP].
Neanderthals have a Supraorbital torus, a prominent, trabecular (spongy) brow ridge.
A portion of tissue that is the most anterior portion of the notochord. The flexural organ secretes Reissner's fiber-related proteins, including F-spondin.
we cannot classify as a secretory circumventricular organ, as this leads to unsatisfiability
may be an ontogenetical remnant of the infundibular organ in cephalochordates
we include a separate class for snake venom glands
A kidney-shaped alveolar glands located in the upper thigh connected by a thin-walled duct to a calcaneus spur, or calcar, on each hind limb.
The female platypus, in common with echidnas, has rudimentary spur buds which do not develop (dropping off before the end of their first year) and lack functional crural glands. Not to be confused with 'calcaneal spur', a small osteophyte (bone spur) located on the calcaneus (heel bone)
The collection of all skeletal elements in an individual limb or fin.
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]
Section of the forelimb skeleton located between the stylopodium and the autopodium.
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
obsoleted as it was already present in GO
obsolete proteinaceous extracellular matrix
Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix.
Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix.
Cartilage tissue that is not mineralized.
add developmental relationships; add disjointness axiom
A commissure that is part of a diencephalon.
An axon tract that is part of a diencephalon.
A tooth that is attached to a maxilla[TAO,modified].
this ontology also contains a class for 'tooth of upper jaw'. This is not equivalent to 'maxillary tooth' in a multi-species context, because many vertebrates have other tooth-bearing bones in the upper jaw[UBERON:cjm]
Tooth that is attached to the maxilla.[TAO]
Tooth that is attached to a dentary/mandible[TAO,modified].
Note that we treat dentary tooth and mandibular tooth as equivalent
Tooth that is attached to the dentary.[TAO]
relationship loss: part_of dentary tooth row (TAO:0001952)[TAO]
there are two jaw regions: the upper and lower. Each jaw region can be subdivided into left and right halves
Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species).
The long ventral process of the incus which articulates with the stapes
the lenticular process may be homologous to the shaft of the stapes and result from fusion of the former quadrate- stapes articulation. This speculation is consistent with the observation that artiodactyls have a very short lenticular process (Thewissen & Hussain (1993)), with perhaps greater length to the corresponding process of the stapes
A gingiva that is part of a upper jaw region.
A gingiva that is part of a lower jaw region.
Tooth that is attached to a coronoid bone.
An extension of the sternum (breastbone) which runs axially along the midline of the sternum and extends outward, perpendicular to the plane of the ribs[WP].
'A muscle in the bird's thorax region that originates from carina of the sternum, furcula, and sternal ribs and inserts onto proximal dorsal surface of the humerus. It acts as a primary elevator of the wing in upstroke. [Manual of Ornithology: Avian Structure and Function, by Proctor and Lynch, 1998].
Replacement bone that is bilaterally paired and (in teleosts) articulates with the neurocranium dorsally and the opercle posteriorly[TAO,modified].
Replacement bone that is bilaterally paired and articulates with the neurocranium dorsally and the opercle posteriorly.[TAO]
relationship loss: overlaps hyomandibula-metapterygoid joint (TAO:0001979)[TAO]
relationship loss: overlaps hyomandibula-opercle joint (TAO:0005265)[TAO]
relationship loss: overlaps preopercle vertical limb-hyomandibula joint (TAO:0005278)[TAO]
In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally.
Cartilage form of the hyomandibular element.
Pharyngeal arch cartilage that is bilaterally paired and articulates with the chondrocranium dorsally, the opercle bone posteriorly, and the palatoquadrate cartilage anteriorly.[TAO]
The upper paired deep bone or cartilage of the hyoid region, sometimes taking part in jaw suspension and which supports the opercle. Dorsally it articulates with the otic capsule at the hyomandibular fossa, ventrally with the quadrate and symplectic. In most Teleostei it has a foramen for the hyomandibular branch of the facial nerve (VII).
In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally.[TAO]
Pharyngeal arch cartilage that is bilaterally paired and the largest cartilaginous component of the ventral hyoid arch.[TAO]
relationship loss: overlaps ceratohyal-branchiostegal ray joint (TAO:0001850)[TAO]
relationship loss: overlaps dorsal hypohyal-urohyal joint (TAO:0001847)[TAO]
relationship loss: overlaps epihyal-branchiostegal ray joint (TAO:0001849)[TAO]
relationship loss: overlaps inter-ventral hypohyal joint (TAO:0001846)[TAO]
relationship loss: overlaps interhyal-epihyal joint (TAO:0001841)[TAO]
relationship loss: overlaps ventral hypohyal-urohyal joint (TAO:0001848)[TAO]
Replacement bone that is bilaterally paired and articulates with the hypohyal cartilage or bone, dorsal and ventral hypohyals, and posterior ceratohyal posteriorly.[TAO]
relationship loss: overlaps ceratohyal-dorsal hypohyal joint (TAO:0001843)[TAO]
relationship loss: overlaps ceratohyal-ventral hypohyal joint (TAO:0001844)[TAO]
relationship loss: overlaps epihyal-ceratohyal joint (TAO:0001842)[TAO]
Pharyngeal arch cartilage that is bilaterally paired and articulates posteriorly with the ceratohyal cartilage.[TAO]
The hypohyal is a ventral element of the hyoid arch which links the ceratohyal and the basihyal.
Skeletal element that is median and is the anterior-most element of the ventral hyoid arch.
Pharyngeal arch cartilage that is median and is the anterior-most cartilage of the ventral hyoid arch.
Replacement bone that is median and is the anterior-most bone of the ventral hyoid arch.
This is the paired bone that makes up the segment of the mammalian hyoid apparatus connecting the epihyoids with the skull via the tympanohyoid cartilages on each side. Ventrally, it defines the medial and lateral compartments of the guttural pouch in the horse.
The stylohyoid bone is one of the four bones ( stylohyoid, ceratohyoid, basihyoid, thyrohyoid) of the hyoid apparatus in the horse. Other species have five bones, the fifth being the epihyoid that is not present in the horse. The stylohyoid bone in the horse is significantly larger compared to other bones of the hyoid apparatus and divides the guttural pouch into two chambers, medial and lateral. The hyoid apparatus consists of a series of bony rods, jointed together and forming a means of suspending the tongue and larynx from the skull
A projection on the basihyal bone. Laterally the lingual process is compressed. It has a blunt pointed free end, and its lateral surfaces are slightly concave. The dorsal border is thin and irregular, and the ventral border is thick and rough. In the living animal the lingual process is embedded within the root of the tongue.
This small finger of cartilage completes the connection between the thyrohyoid bone and the thyroid cartilage (rostral cornu)
Is a laterally bowed, sagittally compressed, slender element that extends from dorsocaudally from the lateral parts of the basihyoid. It connects the basiohyoid with the rostral corner of the thyroid cartlilage of the larynx.
The superior horn of thyroid cartilage is long and narrow, directed upward, backward, and medialward, and ends in a conical extremity, which gives attachment to the lateral hyothyroid ligament.
The inferior horn of thyroid cartilage is short and thick; it is directed downward, with a slight inclination forward and medialward, and presents, on the medial side of its tip, a small oval articular facet for articulation with the side of the cricoid cartilage.
The terminal segment in the chain of skeletal elements of the hyoid apparatus. One of a pair of rods of cartilage that connect the hyoid bone to the styloid process of the petrous part of the temporal bone
A zone of the frontal bone that consists of two thin triangular plates, the orbital plates, which form the vaults of the orbits, and are separated from one another by a median gap, the ethmoidal notch.
A palatal bone which -- like many palatal bones -- may originally have developed as a dermal bone replacing part of the palatoquadrate, the primitive upper jaw. Like the palatine (also called dermopalatine), the ectopterygoid replaces the middle part of the autopalatine. It may be serially homologous with the palatine(s), but is somewhat specialized, being the last (most posterior in palatal view) of the series and bordering the fossa for the jaw muscles. In a typical tetrapod it abuts the palatine anteriorly, the maxilla laterally, the pterygoid or the fossa mandubuaris medially, and the fossa posteriorly
Dermal bone that forms the lateral border of the palate and articulates with the quadrate posteriorly, the entopterygoid medially and the dermopalatine and/or autopalatine antero-laterally. The ectopterygoid is a paired bone.[TAO]
The ectopterygoid is often toothed.[TAO]
taken from TAO but is present in tetrapods
The splenial is a small bone in the lower jaw of reptiles, amphibians and birds, usually located on the lingual side (closest to the tongue) between the angular and suprangular.
The surangular is a dermal bone of the lower jaw. It typically covers much of the dorsal and lateral surface of the posterior jaw and variably extends onto the medial (inside) surface. The surangular articulates with and supports the articular, which forms the jaw joint with the quadrate in most vertebrates, and is in turn supported by the angular. More distally, the surangular bridges the mandibular fenestra, if one is present. It may also bear a raised dorsal coronoid process, an important attachment site for the mandibular adductors. At its distal (or rostral) end, the surangular meets the dentary, the main tooth-bearing bone of the lower jaw in most vertebrates.
In some lepospondyls, and in frogs and salamanders, the surangular is absent. However, it becomes increasingly significant in the anthracosaur lineage. In turtles, it is one of the two principle bones of the lower jaw. In lepidosaurs, it is less important because of the development of a separate coronoid bone. In advanced lizards and pythonomorphs, it may fuse with the articular and perhaps other bones and loses its separate identity. In syanapsids, a secondary jaw joint develops between the surangular and the squamosal, which becomes the unique mammalian jaw articulation. However, the surangular fuses with the dentary and becomes the unitary mammalian 'mandible' without a separate identity
Nevertheless, it is not completely clear that this[osteichthyans] surangular is homologous with the surangular in tetrapods
Osseous element of intramembranous origin that extends along the lingual margin of Meckel's cartilage.
An anuran dermal bone that usually is paired and roofs the braincase.
A fold that lies between the mouth and pharynx and marks the posterior border of the mouth
An odontogenic papilla that is part of a molar tooth [Automatically generated definition].
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
A single large dorsal limb rotator muscle in lower tetrapods that runs from the lumber region and girdle to the femur.
3 muscles differentiate from this: psoas, iliacus and pectineus.
A single large ventral muscle in lower tetrapods that runs from the pubis and aschium to the femur.
obturator externus and quadratus femoris are derivatives
Limb extensor that runs from ilium to femur.
A muscle of the patagium that attaches to the clavicle and the metacarpal
Homolog of levator operculi and epihyoidean - or in mammals, the stapedius (the digastric opens the jaws)[Kardong] The (sphenodon) m. Depressor Mandibulae originates from the posterodorsal edge of the parietal and squamosal, and from a small mid-line portion of connective tissue
Hyoid muscle that originates at the ventrolateral margin of the pterotic and inserts in the dorsomesial edge of the opercle. The levator operculi is responible for jaw depression, its force of contraction is transmitted through the opercular series and the interoperculo-mandibular ligament to the lower jaw.
Muscle in sharks that is homologous to levator operculi and depressor mandibulae / stapedius
Ventral head of a bicapitate rib. It articulates with the parapophysis[AAO].
Ribs of primitive tetrapods are bicipital (having two heads)
Dorsal head of a bicapitate rib. It articulates with the diapophysis[AAO].
sometimes called the tuberculum, but not to be confused with the tubercle, which is between body and neck
Paired processes that arise near the midpoint of the neural arch lamina, for the attachment of the tuberculum of two-headed ribs. Also called transverse processes. In anurans, the term diapophysis is used in reference to the modified transverse processes of the sacral vertebra elaborated for support of the pelvic girdle.
taken from AAO, requires attention of amphibian anatomy experts, in particular, relationship to transverse processes
Dermal bone of pectoral girdle that is median and ventral in position.
See discussion on pectoral girdles - change relationship to overlaps? Kardong: enlarged oval scale
Present in therapids and monotremes, reduced in size in marsupials and placentals. In birds, the interclavicle is fused with the clavicles to form the furcula (wishbone); the furcula forms a 'Y' shape and the interclavicle is the stem of the 'Y'.
Fused ventral dermal element constituting the plastron.
Paired dermal bone that is part of the anterior region of the plastron. The epiplastron is found only in turtles. [PHENOSCAPE:ad].
A median bone at the anterior margin of the plastron.
A paired plastron element that is in the posterior part of the plastron, anterior to the xiphiplastron and posterior to the hyoplastron
A paired plastron element that is in the posterior part of the plastron, posterior to the hypoplastron
Fused dorsal element constituting the carapace of a turtle shell.
The carapace contains a mix of dermal bone and rib cage
One of a series of bones around the edge of the carapace.
One of eight pairs of plates on the carapace, forming two rows adjacent to the peripheral plates.
A combination of ribs and fused dermal bone
One of a series of plates on the dorsal midline of the turtle shell, posterior to the nuchal bone.
In many species of Pleurodire they are submerged below the pleurals
One of three plates on the posterior end of the carapace, posterior to the neural plates.
A plate that lies between the posteriormost neural plate and the pygal plate.
Enlarged section of perichordal tube that is arranged serially but out of phase with segmental musculature.
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly.
Post-Weberian vertebrae lacking hemal spines (Weitzman, 1962), refers generally to the anterior vertebral region bounding the abdominal cavity. Alternate but not quite synonymous terms are abdominal or trunk vertebrae, which bear parapophyses and ribs. In many actinopterygians dorsal to the posterior abdominal cavity there are transitional vertebrae lacking ribs but also without hemal spines or sometimes even enclosed hemal arches. The primary definition would identify these vertebrae as precaudal. Bird and Mabee, 2003.[TAO]
in TAO this is defined as post-Weberian, this may not precisely align with the definition of being part of the trunk
A proximal tarsal bone that articulates with the fibula.
The amphibian intermedium forms part of the astragalus in amniotes[http://www.science.marshall.edu/okeefef/PDFS/OKeefe_et_al_2006_JMorph.pdf]
A tarsal bone that connected_to a hindlimb zeugopod skeleton.
An adductor muscle that acts on the jaw. In some species, this is subdivided into segments based on attachment.
Is a mandibular muscle that forms along the palatoquadrates and inserts on Meckel's cartilages and functions in jaw closing[ZFA:0007049].
In teleosts, the complex is composed of several derived muscles that attach to different parts of the highly kinetic skull.
A muscle derivative of the mandibular levator that runs from the chondrocranium to the palatoquadrate cartilage. Found in sharks
In some fishes such as the chimera and in tetrapods the palatoquadrate becomes fused to the braincase and this muscle is absent.
A jaw muscle arises near the orbit and tapers as it passes posteriorly to its insertion on the adductor mandibulae. Found in sharks.
Odontoid tissue that is avascular non-mineralized matrix that is deposited by odontoblasts and ameloblasts that are excluded from the matrix.
Skeletal tissue that is hypermineralized and aprismatic and deposited by a combination of ameloblasts and odontoblasts that are excluded from the matrix. Enameloid develops from pre-enameloid tissue.
extraembryonic portion of umbilical artery
Each of the two arteries arising from the hypogastric arteries of the fetus and passing throught the umbilical cord to the placenta.
Each of the two arteries arising from the hypogastric arteries of the fetus and passing throught the umbilical cord to the placenta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
A cardiovascular system that is part of a conceptus.
Portion of midgut after it bends around the superior mesenteric artery
A hepatic sinusoid that is part of a caudate lobe of liver.
liver right caudate lobe hepatic sinusoids
A hepatic sinusoid that is part of a quadrate lobe of liver.
liver right quadrate lobe hepatic sinusoids
A cardiac valve leaflet that is part of a aortic valve.
Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[uncertain][VHOG]
A cardiac valve leaflet that is part of a pulmonary valve.
Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum
todo - add parthood relationships to tubercles
A genital swelling that is part of a female reproductive system.
A genital swelling that is part of a male reproductive organ.
Lymphatic vessels develop from lymph sacs that arise from developing veins, which are derived from mesoderm. The first lymph sacs to appear are the paired jugular lymph sacs at the junction of the internal jugular and subclavian veins.
Lymphatic vessels develop from lymph sacs that arise from developing veins, which are derived from mesoderm. The first lymph sacs to appear are the paired jugular lymph sacs at the junction of the internal jugular and subclavian veins. [http://en.wikipedia.org/wiki/Lymphatic_system][VHOG]
Lymph hearts are pulsatile organs, present in lower vertebrates, that function to propel lymph into the venous system. Although they are absent in mammals, the initial veno-lymphatic plexus that forms during mammalian jugular lymph sac development has been described as the vestigial homologue of the nascent stage of ancestral anterior lymph hearts.[well established][VHOG]
The left RLN is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]
vagus X nerve left recurrent laryngeal branch
vagus X nerve right recurrent laryngeal branch
The stalk emanates from the diencephalic roof at a left-of-medial position.[TAO]
The epithalamus contains the epiphysis (pineal gland and related structures), which is located at the end of a stalk, the epiphyseal stalk.[well established][VHOG]
Anatomical projection that is composed of cartilage tissue.
Paired, cylindrical, and small bones of endochondral origin that lie anteromedial to the anterior end of Meckel's cartilage. The precursors of the mentomeckelian bones are the larval infrarostral cartilages.
Anatomical structure that is part of the larva.
An anatomical space that is part of a bone of lower jaw.
An anatomical space that is part of a bone of upper jaw.
A duct connecting the the utricle to the saccule in the membranous labyrinth of the ear.
utricosaccular duct of membranous labyrinth
Alternate: leads from the utricle of the internal ear to the endolymphatic duct. - http://medical-dictionary.thefreedictionary.com/utriculosaccular+duct. We assume a 3-way connection
A cranial nerve nucleus that is associated with a vagus nerve.
Nucleus of neuraxis which is located within the spinal cord. Example: dorsal nucleus of Clarke, Intermediolateral nucleus.
in ZFA this is the superclass of dorsolateral and medial (which have not been generalized above ZFA). In this ontology it is a broad grouping class covering these zebrafish structures as well as the generalized dorsal motor nucleus
A small tubular invagination of the skin with a fleshy dermal papilla at the bottom from which the feather grows. The papilla is inserted in the opening at the end of the quill[TMD]. Forms by invagination of cylinder of epidermal tissue at base of feather bud.
The follicle consists of a series of tissue layers (from peripheral to central), including the dermis of the follicle, the epidermis of the follicle (outer epidermal layer), the follicle cavity or lumen (the space between epidermal layers), the follicle (epidermal) collar (or inner epidermal layer), and the dermal pulp (tissue at the center of the follicle). The proliferation of feather keratinocytes and most of the growth of the feather occurs in the follicle, or epidermal, collar (From: Prum 1999).
An epidermal thickening above a condensation of dermal cells that will give rise to a feather follicle
Similar to erector pili muscles of mammals; attached to the sides of the follicle; capable of elevating or lowering entire groups of feathers.
A flight feather that lies along a single horizontal row on the rear margin of the anatomical tail. Only the central pair are attached (via ligaments) to the tail bones; the remaining rectrices are embedded into the rectricial bulbs, complex structures of fat and muscle that surround those bones. Rectrices are always paired, with a vast majority of species having six pairs. They are absent in grebes and some ratites, and greatly reduced in size in penguins
A flight feather located on the posterior side of the wing
A remex feather that is connected to the manus
these are the longest and narrowest of the remiges (particularly those attached to the phalanges), and they can be individually rotated. These feathers are especially important for flapping flight, as they are the principal source of thrust, moving the bird forward through the air. Most thrust is generated on the downstroke of flapping flight. However, on the upstroke (when the bird often draws its wing in close to its body), the primaries are separated and rotated, reducing air resistance while still helping to provide some thrust
A remex feather that is connected to the ulna.
In some species, the ligaments that bind these remiges to the bone connect to small, rounded projections, known as quill knobs, on the ulna; in other species, no such knobs exist. Secondary feathers remain close together in flight (they cannot be individually separated like the primaries can) and help to provide lift by creating the airfoil shape of the bird's wing. Secondaries tend to be shorter and broader than primaries, with blunter ends
A remex feather that is connected to the humerus.
tertials are connected to the humerus in some species. These elongated "true" tertials act as a protective cover for all or part of the folded primaries and secondaries, and do not qualify as flight feathers as such. However, many authorities use the term tertials to refer to the shorter, more symmetrical innermost secondaries of passerines (which perform the same function as true tertials) in an effort to distinguish them from the other secondaries.
An anatomical cavity that is part of a feather shaft.
A tissue that is part of a cavity of feather shaft.
A suprabasal cell population which together with the feather follicle placode develops into the feather follicle.
The development of placodes where dermal condensations occur, an evolutionary novelty, required changes in gene expression and timing. However, such changes are known to be an important mechanism in the origin of morphological innovations in many other organisms (True and Carroll 2002, Prum 2005)
The part of the feather bud formed by a proliferation of dermal cells
An epithelial bud that is part of a feather bud.
A tissue that is part of a dermis and is part of a feather follicle.
A tissue that is part of a epidermis and is part of a feather follicle.
outer epidermal layer of feather follicle
The proliferation of feather keratinocytes and most of the growth of the feather occurs here
inner epidermal layer of feather follicle
An anatomical cluster that consists of feathers.
Superficial fascia is found in the subcutis in most regions of the body, blending with the reticular layer of the dermis. It is present on the face, over the upper portion of the sternocleidomastoid, at the nape of the neck, and overlying the sternum. It is comprised mainly of loose areolar connective tissue and adipose and is the layer that primarily determines the shape of a body. In addition to its subcutaneous presence, this type of fascia surrounds organs and glands, neurovascular bundles, and is found at many other locations where it fills otherwise unoccupied space. It serves as a storage medium of fat and water; as a passageway for lymph, nerve and blood vessels; and as a protective padding to cushion and insulate. Superficial fascia is present, but does not contain fat, in the eyelids, ear, scrotum, penis and clitoris.
we follow FMA, BTO, NCIT and WP in making this a distinct class from hypodermis.
A tube lumen that is part of a atrioventricular canal.
Zone of continuity which connects the cardiac atrium to the cardiac ventricle.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
Lobular organ the parenchyma of which consists of glandular acini which communicate with the vestibule of vagina. Examples: right vestibular gland, lesser vestibular gland.
A sebaceous glands in the areola surrounding the nipple.
Lobular organ the parenchyma of which consists of acini connected to the surface of the areola or to a lactiferous duct by the duct of areolar gland. Examples: There are variable numbers of areolar glands[FMA:58090].
A duct that is part of a minor vestibular gland.
A duct that is part of a vestibular gland.
A duct that is part of a sebaceous gland.
An acinus that is part of a sebaceous gland.
An acinus that is part of a parotid gland.
An acinus that is part of a salivary gland.
An acinus that is part of a areolar gland.
An acinus that is part of a mammary gland.
An acinus that is part of a lacrimal gland.
An acinus that is part of a exocrine gland.
The internal auditory meatus (also internal acoustic meatus, internal auditory canal, and internal acoustic canal) is a canal in the petrous bone of the temporal bone of the skull that carries nerves from inside the cranium towards the middle and inner ear compartments namely cranial nerve VII and cranial nerve VIII.
Alternate def: The internal acoustic meatus (or internal auditory meatus ) is an opening on the medial surface of the petrous temporal bone. It is through this passageway that the facial nerve (cranial nerve VII) and vestibulocochlear nerve (cranial nerve VIII) pass to reach their sites of innervation. The vestibulocochlear nerve divides at the internal acoustic meatus to continue as separate vestibular and cochlear components. [MURDOCH:908]
the FMA class specifically refers to ureter
The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity
In a condyloid joint (condyloid articulation, ellipsoidal joint) an ovoid articular surface, or condyle, is received into an elliptical cavity. This permits movement in two planes, allowing flexion, extension, adduction, abduction, and circumduction.
Wikipedia says pisiform and triquetral- todo check pisotriquetral
A cranial suture that connects a nasal bone and connects a maxilla.
articulation of the nasal bone with maxilla
A synarthrosis is a type of joint which permits very little or no movement under normal conditions. Most synarthrosis joints are fibrous. Suture joints and synchondroses are synarthroses.
Amphiarthrosis is a type of continuous, slightly movable joint.
A skeletal ligament that is part of a sternoclavicular joint.
The oral part of the tongue anterior to the terminal sulcus.
The lateral border that separates the dorsum from the inferior surface of the tongue on each side, the two borders meeting anteriorly at the apex..
A muscle layer that is part of a wall of esophagus.
In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle
The testes, at an early period of fetal life, are placed at the back part of the abdominal cavity, behind the peritoneum, and each is attached by a peritoneal fold, the mesorchium, to the mesonephros.
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
Fluid of the ganglia and peripheral nerves that lie outside the brain and spinal cord
A organ cavity that is part of a vagina.
A layer of connective tissue that ensheaths a muscle fiber and is composed mostly from reticular fibers. It also contains capillaries, nerves and lymphatics. The term cardiac skeleton is sometimes considered synonymous with endomysium, but sometimes it refers to the combination of the endomysium and perimysium.
Reticular tissue which surrounds a smooth muscle cell.
Reticular tissue which surrounds a cardiac myocyte.
Fibrocollagenous sheath of cardiac muscle cell
Reticular tissue which surrounds a skeletal muscle cell.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
The fibrous sheath enveloping each of the primary bundles of skeletal muscle fibers.
The hair matrix surrounds the top and sides of the dermal papilla. The hair matrix cells give rise to 6 different types of cells that make up the different layers of the hair shaft and the inner root sheath.
A smooth muscle tissue that is part of a gizzard.
A rock held inside a gastrointestinal tract.
Plantaris is a vestigial structure and one of the superficial muscles of the posterior crural compartment of the leg. It is innervated by the tibial nerve (S1, S2) . It is composed of a thin muscle belly and a long thin tendon. It is approximately 2-4 inches long, and is absent in 7 - 10% of the human population. It is one of the plantar flexors in the superior compartment of the leg along with the gastrocnemius, and soleus. The plantaris is considered an unimportant muscle, it mainly acts with gastrocnemius[WP].
todo - coordinate with phenoscape-ext on representation of amphibian plantaris longus and profundus
Mammalian gastrocnemius medialis and flexor hallucis longus arise from reptilian gastrocnemius internus[Kardong]
Mammalian gastrocnemius lateralis, soleus and plantaris arise from reptilian gastrocnemius externus[Kardong]
A muscle of lower tetrapods that covers much of the lower leg and retracts it. Homologous to mammalian gracilis
An intertwined cluster of nerve fibers surrounded by glia where mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons
Synaptic structure found in thalamic relay nuclei consising of a complex of afferent terminals, relay cell dendrites, interneuron dendrites and other processes. These complexes are surrounded by astrocytic processes.
The thickened peripheral margin of the vitreous membrane of the cornea.
masses of developing blood cells attached to endothelium in the yolk sac
in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels
The the continuous basement membrane found within the membranous labyrinth of the cochlea, known to extend from the limbus, down to the inner sulcus, across the basilar membrane, up to the external sulcus to the spiral prominence and radiating into the spiral ligament ensheathing the root cell processes
Nerve fibers which project from cell bodies of autonomic ganglia to synapses on target organs.
Nerve fibers which project from the central nervous system to autonomic ganglia. In the sympathetic division most preganglionic fibers originate with neurons in the intermediolateral column of the spinal cord, exit via ventral roots from upper thoracic through lower lumbar segments, and project to the paravertebral ganglia; there they either terminate in synapses or continue through the splanchnic nerves to the prevertebral ganglia. In the parasympathetic division the fibers originate in neurons of the brain stem and sacral spinal cord. In both divisions the principal transmitter is acetylcholine but peptide cotransmitters may also be released.
A noradrenergic or adrenergic axonal fiber projecting from a sympathetic ganglion to an effector organ
A cholinergic axonal fiber projecting from the CNS to a sympathetic ganglion
A cholinergic axonal fiber projecting from a parasympathetic ganglion to an effector organ
A cholinergic axonal fibers projecting from the CNS to a parasympathetic ganglion
An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle
A pilosebaceuous init that contains a strand of virbissa hair (a specialized tactile hair) with the follicle incorporating a blood sinus, heavily innervated by sensory nerves.
MA has distinct classes for vibrissa and vibrissa hair - the former includes the follicle and is thus not the hair proper. We model this as the 'vibrissa unit'
A bulb of hair follicle that is part of a vibrissa unit.
A hair root sheath that is part of a vibrissa unit.
A hair inner root sheath that is part of a vibrissa unit.
A hair outer root sheath that is part of a vibrissa unit.
An arrector muscle of hair that is part of a vibrissa hair.
An angle of the scapula that is broad and bears the glenoid cavity or fossa[WP,unvetted].
A luminal layer of epithelium that is part of a ureter.
A luminal layer of epithelium that is part of a endometrium epithelium.
A luminal layer of epithelium that is part of a mammary gland.
lumina layer of epithelium of lactiferous gland
A luminal layer of epithelium that is part of a prostate gland.
subdivision of luminal layer of epithelium of prostatic gland
A stomach region that has_part a stomach glandular epithelium.
A stomach region that has_part a stomach non-glandular epithelium.
A hepatic vein that is part of a left lobe of liver.
A hepatic vein that is part of a right lobe of liver.
A ring of cartilage that surrounds the acetabulum[WP,unvetted].
Cartilaginous ring that forms the entire acetabular margin[AAO:0000864].
Its function is to deepen the acetabulum, making it more difficult for the head of the femur to slip out of place (sublux)
some sources treat this as fibrocartilage
A ring of fibrocartilage attached to the margin of the glenoid cavity of the scapula.
consider classifying as 'annulus fibrosus'
An articular capsule that is part of the glenohumeral joint.
An articular capsule that is part of the hip joint.
The transverse tarsal joint is formed by the articulation of the calcaneus with the cuboid, and the articulation of the talus with the navicular. The movement which takes place in this joint is more extensive than that in the other tarsal joints, and consists of a sort of rotation by means of which the foot may be slightly flexed or extended, the sole being at the same time carried medially (inverted) or laterally.
The talocalcaneonavicular articulation is an arthrodial joint: the rounded head of the talus being received into the concavity formed by the posterior surface of the navicular, the anterior articular surface of the calcaneus, and the upper surface of the plantar calcaneonavicular ligament. There are two ligaments in this joint: the articular capsule and the dorsal talonavicular.
Calcaneocuboid Articulation (articulation of the calcaneus with the cuboid). The ligaments connecting the calcaneus with the cuboid are five in number, viz. , the articular capsule, the dorsal calcaneocuboid, part of the bifurcated, the long plantar, and the plantar calcaneocuboid.
In a saddle joint (sellar joint, articulation by reciprocal reception) the opposing surfaces are reciprocally concave-convex.
The early union, by hyaline cartilage, of the manubrium and the body of the sternum, which later becomes a symphysial type of joint.
The facet of the tubercle of the rib forms an articulation with the adjacent transverse process of a thoracic vertebra. This is a plane type synovial joint called the costotransverse joint. This articulation is present in all but the eleventh and twelfth ribs. Ribs 1 to 10 have two joints in close proximity posteriorly; the costovertebral joints and the costotranseverse joints. This arrangement restrains the motion of the ribs allowing them to work in a parallel fashion during breathing. If a typical rib had only one joint posteriorly the resultant swivel action would allow a rib to be non-parallel with respect to the neighboring ribs making for a very inefficient respiratory mechanism. The ventral rami innervate the costotransverse joints. Therefore, therapeutic medial branch blocks are ineffectual. The ligaments of the joint are: Articular capsule Posterior costotransverse Anterior costotransverse Ligament of the neck of the rib Ligament of the tubercle of the rib
A skeletal joint that connects a radius bone and connects a carpal skeleton.
An ankle joint that passes between the proximal and distal tarsals.
Calcaneus and astragalus are interlocked, line of flexion is distal to them[Kardong]
A skeletal ligament that connects the fibula to the talus. Examples: anterior and posterior talofibular ligament
A skeletal ligament that connects the fibula to the calcaneus
In humans, it is a narrow, rounded cord, running from the apex of the fibular malleolus downward and slightly backward to a tubercle on the lateral surface of the calcaneus. It is covered by the tendons of the Peronæi longus and brevis.
A skeletal ligament that connects a tibia and connects a tarsal skeleton.
deltoid collateral ligament of ankle joint
ligamentum collaterale mediale (articulatio talocruralis)
ligamentum deltoideum (articulatio talocruralis)
medial collateral ligament of ankle joint
An epiphysis that is part of a phalanx of a pes [Automatically generated definition].
An epiphysis that is part of a proximal phalanx of pes.
An epiphysis that is part of a middle phalanx of pes.
An epiphysis that is part of a distal phalanx of pes.
An epiphysis that is part of a proximal phalanx of manus.
An epiphysis that is part of a middle phalanx of manus.
An epiphysis that is part of a distal phalanx of manus.
A joint that connects the bones of the crus to the proximal tarsal bones
an ankle joint that passes between the astragalus and calcaneum[Palaeos].
line of flexion between calcaneus and astragalus
An air-filled recess in the head of birds which lies lateral to the nasal cavity into which it opens
A mucosa that adjacent_to a infraorbital sinus.
The structure that contains the coelemic cavity.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
A bronchiole that is part of a lower lobe of left lung.
A bronchiole that is part of a upper lobe of left lung.
A bronchiole that is part of a lower lobe of right lung.
A lobar bronchus that is part of a middle lobe of right lung.
lobar bronchus of right lung middle lobe
A lobar bronchus that is part of a upper lobe of left lung.
A lobar bronchus that is part of a lower lobe of left lung.
A bronchiole that arises from a segmental bronchus and does not contain cartilage.
A bronchiole that is part of a middle lobe of right lung.
A tooth that is on the roof of the mouth.
this is distinct (but not disjoint) from palatine bone
A tooth that is attached to a palatine bone.
Teeth present in some fishes on the palatine bones, bones that lie inside the upper jaw bones (sometimes maxillaries, sometimes premaxillaries) usually behind the vomerine tooth patch.
A subdivision of skeletal system that subdivision_of a hard palate.
Bone that forms as a replacement of another structural tissue.
Bone that forms as a replacement of another structural tissue.[TAO]
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
A skeletal joint that connects a tibia and connects a talus.
see also FMA:44063 ! tibiotalar part of medial ligament of ankle joint
The surface of the head of the femur is smooth, coated with cartilage in the fresh state, except over an ovoid depression, the fovea of head of femur, which is situated a little below and behind the center of the head, and gives attachment to the ligamentum teres.
proximodistal trajectory through a metapterygium[Wagner]
persisted in sacropterygians, precursor to limb axis
A cartilaginous condensation that has_potential_to_develop_into a patella.
Note some sources have this as intramembranous
A pre-cartilage condensation that has_potential_to_develop_into a patella.
An anatomical cavity that is part of a bronchus.
An anatomical cavity that is part of a main bronchus.
An anatomical cavity that is part of a lobar bronchus.
An anatomical cavity that is part of a segmental bronchus.
An anatomical cavity that is part of a parabronchus.
An extension of the parabronchus, the walls of which are the site of gas exchange
One of of three muscles associated with the uncinate processes.
The period spanning the range immediately before and after birth
In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes
A salivary gland that is part of a cheek.
Cooper's ligaments (also known as the suspensory ligaments of Cooper and the fibrocollagenous septa) are connective tissue in the breast that helps maintain structural integrity. Transmission diffraction tomography can reveal the anatomy. Cooper's Suspensory Ligament should not be confused with the pectineal ligament (sometimes called the inguinal ligament of Cooper) which shares the same eponym.
Connects skin of mammary gland with deep fascia
a coffee bean-shaped constant, large and regular bone. The lateral surface of the bone is convex in all directions and non-articular. The medial surface is covered with hyaline cartilage and articulates by means of a synovial joint with the corresponding facet of the cuboid bone. The histological structure and the mode of ossification of the os peroneum are identical to that of other short bones of the skeleton.
sesamoid bone of the peroneus longus muscle
A keratinous sieve composed of bristles that enables filter feeding in the mouth of mysticete whales.
A keratinous bristle that enables filter feeding in the mouth of mysticete whales.
A strut formed from the union of the zygomatic process of the frontal bone with the frontal process of the zygomatic bone.
The part of the zygomatic process consisting of the frontal bone[WP]
A space or gap between two teeth. Many species of mammals have diastemata as a normal feature, most commonly between the incisors and molars.
Body substance, which consists of food admixed with saliva contained in the oral cavity, pharynx or esophagus[FMA].
FMA def restricts this to 'oral cavity, pharynx or esophagus', but child terms includes chyme - which is in the stomach
Ingested food has been chewed at the point of swallowing.
A bolus of semi-degraded food regurgitated from the reticulorumen of a ruminant, produced during the physical digestive process of rumination
A dental structure found in some mammals, comprising a group of front teeth arranged in a manner that facilitates grooming.
The toothcomb occurs in lemuriform primates (which includes lemurs and lorisoids), treeshrews, colugos, hyraxes, and some African antelopes. The structures evolved independently in different types of mammals through convergent evolution and vary both in dental composition and structure. In most mammals the comb is formed by a group of teeth with fine spaces between them. The toothcombs in most mammals include incisors only, while in lemuriform primates they include incisors and canine teeth that tilt forward at the front of the lower jaw, followed by a canine-shaped first premolar. The toothcombs of colugos and hyraxes take a different form with the individual incisors being serrated, providing multiple tines per tooth
Any of the passages admitting nutrient vessels to the medullary cavity of bone
An anatomical space that is part of a nutrient foramen conduit, leading to the medullary cavity of the bone.
The infraspinatus muscle inserts at this tendon to the distal greater tubercle of the humerus. This tendon stretches across the shoulder joint to attach to the humerus and in doing so acts as a very strong ligament to hold the joint surface in apposition. This structure restricts the movement of the shoulder joint to flexion and extension (together with the suscapularis tendon and the supraspinatus tendon). A bursa lies under this tendon at the greater tubercle of the humerus. The bursa is lined by a synovial membrance and filled with synovial fluid and protects the infraspinatus tendon and the shoulder joint by allowing the transmissions of tension and sheer forces around an angle.
A tendon which emerges from the distal end of the humerus and follows the posterior margin of the wing, attaching at the distal end of digit 2. The raches of the remiges (i.e., the stems of the flight feathers) are stabilized by passing through the vinculum.
Organ component cluster which consists of a tendinous vinculum surrounded by synovial membrane of the synovial tendon sheath. Examples: short vinculum of tendon of flexor digitorum superficialis, long vinculum of tendon of flexor digitorum profundus.
This is not classified as a tendon in FMA
A respiratory pump found in basal craniates
this is restricted to hagfishes; structure with same name found in tunicates.
Muscular scroll-like flap that moves water through median nostril and over gills
trifid and posteriorly directed lamina arising from roof of pharynx, behind posterior end of naso-pharyngeal duct;
May correspond to radiale[Origin and evolution of birds, Feduccia]
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
One of two elements that constitute the basal row of tarsals. The fibulare constitutes the preaxial element[AAO].
One of two element that constitute the basal row of tarsals. The fibulare constitutes the preaxial element. In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the tibiale.[AAO]
In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the tibiale
A minute hook that projects off of a feather barbule, holding barbules together
Outermost point on an external nose or snout
Hemispherical ball located at the lower end of the humerus that stands out prominently from the surrounding structures toward the flexor surface of the forelimb
Hemispherical ball located at the lower end of the humerus that stands out prominently from the surrounding structures toward the flexor surface of the forelimb and fits into the socket joint of the olecranon process[AAO].
A deep evacuation in the bone, into which the anconeal process of the ulna passes when the elbow joint is extended.
Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE].
This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus
the FMA term is under 'general anatomical term'.
The intercuneiform articulations are articulations among the cuneiform bones[WP,unverified].
The term 'cuneocuboid articulation' is sometimes used to describe the joint between the cuboid and lateral cuneiform, but this term isn't recognized by Terminologia Anatomica
intercuneiform and cuneocuboid articulations
lateral-intermediate intercuneiform joint
medial-intermediate intercuneiform joint
A prepollex does not contain phalanges nor does it articulate with a metacarpal. It articulates with elements of the carpal (wrist) skeleton[AAO:DB]. editor note: TODO add articulation relations
A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.
some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod
A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region.
A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region.
A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.
A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton.
A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton.
The Buccal fat pad is one of several encapsulated fat masses in the cheek. It is a deep fat pad located on either side of the face between the buccinator muscle and several more superficial muscles. It should not be confused with the malar fat pad, which is directly below the skin of the cheek. It should also not be confused with jowl fat pads. It is implicated in the formation of hollow cheeks and the nasolabial fold, but not in the formation of jowls.
blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]
Crescent shaped outer zone of the nucleus accumbens, defined by a combination of chemoarchitecture and afferent and efferent connections. The shell is distinguished from the more centrally located core through the notable reduction in staining for the calcium-binding protein calbindin D28K, which is dense in the core and virtually absent in the shell.
A primordium that has_potential_to_develop_into a stomach.
The middle suprarenal arteries (middle capsular arteries; suprarenal arteries) are two small vessels which arise, one from either side of the abdominal aorta, opposite the superior mesenteric artery. They pass laterally and slightly upward, over the crura of the diaphragm, to the suprarenal glands, where they anastomose with suprarenal branches of the inferior phrenic and renal arteries. In the fetus these arteries are of large size.
facio-acoustic ganglion complex VII-VIII
facio-acoustic VII-VIII ganglion complex
acoustico-facial VII-VIII ganglion complex
A vascular, red cutaneous structure attached in a sagittal plane to the dorsum of the skull of domestic fowl. It consists of a base attached to the skull, a central mass called the body, a backward projecting blade and upward projecting points
An apocrine gland that is part of a skin of body.
in MA, this is the superclass of the 3 innominate elements (pelvic girdle bones) and caudal and sacral vertebrae. This class is included to ensure consistency across anatomical ontologies
A zone of skin that is part of a craniocervical region.
Tonsils consist of an extensive system of crypts, which result in a large internal surface. The tonsils contain four lymphoid compartments that influence immune functions, namely the reticular crypt epithelium, the extrafollicular area, the mantle zones of lymphoid follicles, and the follicular germinal centers. In human palatine tonsils, the very first part exposed to the outside environment is tonsillar epithelium.
obsolete term deriving from MA to NCITA mappings.
An ovarian follicle undergoing maturation.
The supratrochlear artery (or frontal artery), one of the terminal branches of the ophthalmic artery, branches off where the ophthalmic travels posterior to the trochlea.
supratrochlear branch of ophthalmic artery
The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins.
The superior intercostal veins are two veins that drain the 2nd, 3rd, and 4th intercostal spaces, one vein for each side of the body.
The intercostal veins are a group of veins which drain the area between the ribs.
Space of compartment of trunk bounded by the upper and lower surfaces of two consecutive ribs.
The posterior intercostal veins are veins that drain the intercostal spaces posteriorly. They run with their corresponding posterior intercostal artery on the underside of the rib, the vein superior to the artery. Each vein also gives off a dorsal branch that drains blood from the muscles of the back. There are eleven posterior intercostal veins on each side. Their patterns are variable, but they are commonly arranged as: The 1st posterior intercostal vein, supreme intercostal vein, drains into the brachiocephalic vein or the vertebral vein. The 2nd and 3rd (and often 4th) posterior intercostal veins drain into the superior intercostal vein. The remaining posterior intercostal veins drain into the azygos vein on the right, or the hemiazygos vein on the left.
The anterior intercostal veins are the veins which drain the anterior intercostal space.
The intercostal lymph nodes (intercostal glands ) occupy the posterior parts of the intercostal spaces, in relation to the intercostal vessels. They receive the deep lymphatics from the postero-lateral aspect of the chest; some of these vessels are interrupted by small lateral intercostal glands.
The superior phrenic vein, i.e. , the vein accompanying the pericardiacophrenic artery, usually opens into the internal mammary vein.
ureteric bud cells that elongate to form a rigid structure (stalk) consisting of polarized epithelial cells without branching; the stalks differentiate into the collecting system of the mature kidney, while the tip cells interact with the adjacent cells of the metanephric mesenchyme, inducing their conversion into nephrons.
network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP]
external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP].
A urethral meatus that is part of a male urethra[Automatically generated definition].
The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis.
ostium urethrae externum (urethra masculina)
the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone
internal urethral orifice of urinary bladder
Raised calluses of cornified epidermis used by the male to hold the female during mating.
A temporary layer between old and new skin that is invalided by white blood cells[Kardong].
A protein fiber composed mainly of fibroin and produced by certain arthropods[WP,modified].
A follicular lumen is the closed cavity within a follicle of the thyroid gland. It is surrounded by follicular cells and filled with colloid, a concentrated solution of thyroglobulin
mucus-secreting glands in the mucosa of the uterine cervix
Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing.
The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium.
distinction between two FMA classes not clear - we merge them here
A glandular epithelium that is part of a uterine cervix.
The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium.
A epithelium that is part of a ectocervix.
The glandular epithelium that lines the endocervix.
Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet
squamo-columnar junction of uterine cervix
squamocolumnar junction of uterine cervix
Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia.
An artery that originates from the abdominal aorta
in Aceola, Digestion is accomplished by means of a syncytium that forms a vacuole around ingested food. There are no epithelial cells lining the digestive vacuole, although there is sometimes a short pharynx leading from the mouth to the vacuole
A manual digit found in Aves that is the most preaxial position and is morphologically similar to digit 1 in the standard tetrapod configuration and develops from embryonic digit 2, with contributions from embryonic digit 1.
Hypothesized to be homologous to manual digit 1 of other tetrapods. Develops from the embryonic digit that is positionally the 2nd, with contributions from the 1st
A manual digit found in Aves that is morphologically similar to digit 2 in the standard tetrapod configuration and develops from embryonic digit 3.
Hypothesized to be homologous to manual digit 2 of other tetrapods
A manual digit found in Aves that is morphologically similar to digit 3 in the standard tetrapod configuration and develops from embryonic digit 4.
Hypothesized to be homologous to manual digit 3 of other tetrapods
The splint bones sit either side of the equine cannon bone. Homologous to metapodium bones 2 or 4
in future this class may be replaced by a more taxon-neutral class grouping metapodial bones 2 or 4
in future this class may be replaced by a more taxon-neutral class grouping metarsal bones 2 or 4
in future this class may be replaced by a more taxon-neutral class grouping metacarpal bones 2 or 4
forestomach - glandular stomach squamocolumnar junction
squamo-columnar junction between forestomach and glandular stomach
squamocolumnar junction with the glandular stomach
The common bile duct and the pancreatic duct together perforate the medial side of the second portion of the duodenum obliquely, some 7 to 10 cm below the pylorus, forming a structure called the major duodenal papilla. The accessory pancreatic duct sometimes pierces it about 2 cm above and slightly in front of these.
The minor duodenal papilla is the opening of the accessory pancreatic duct into the duodenum. It is sometimes absent, and often nonfunctional.
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]
Epithelium that derives from the mesoderm. [Automatically generated definition].
The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands.
Small bodies containing chromaffin cells occurring outside of the adrenal medulla, most commonly near the sympathetic ganglia and in organs such as the kidney, liver, heart and gonads.
A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus.
encapsulated adipose tissue associated with the mammary gland
encapsulated adipose tissue associated with the femur
The animal pole consists of small cells that divide rapidly, in contrast with the vegetal pole below it.
the XAO class is specific to the zygote.
The vegetal pole contains large yolky cells that divide very slowly, in contrast with the animal pole above it.
One of two hemispheres of the embryo at the zygote or blastula stage[WP,modified]
Like many of the early_development classes in this ontology, this class requires review for its applicability across vertebrates. See the tracker item for further discussion.
A epithelial sac that is part of a Rathke's pouch.
A tarsal bone that is formed from the fusion of the central and 4th tarsal bones.
A tarsal bone that is formed from the fusion of the 2nd and 3rd tarsal bones.
A carpal bone that is formed from the fusion of the 2nd and 3rd distal carpal bones.
In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia.
One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly
We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts
A slight elevation flanking the cloacal membrane and derived from a cloacal fold; anal folds form the border of the anus.
The dilated terminal portion of the male spongy urethra located in the glans penis right before the external urethral orifice, also referred to as the most distal pendulous urethra; it is lined by stratified squamous, non-keratinizing epithelium; during development, the glans of the penis is initially solid but cannulates to give rise to the navicular fossa.
fossa navicularis urethrae (pars spongiosa, urethra masculina)
navicular fossa of spongiose part of urethra
An inconstant fold or valve of mucous membrane sometimes found in the root or upper wall of the navicular fossa of the urethra
A longitudinal mucosal fold in the dorsal wall of the urethra[MP]
in the FMA this is part of the prostatic urethra - but this leads to inconsistencies as 'urethral crest' in sex-neutral, with male and female subtypes
narrow longitudinal fold of mucosa on the posterior wall of the male urethra, extending from the uvula of the bladder through the prostatic urethra; when distended, it may serve to prevent the passage of the semen backward into the bladder; on either side of the male urethral crest is a slightly depressed fossa, the prostatic sinus, the floor of which is perforated by the orifices of the prostatic ducts from the lateral lobes of the prostate; the ducts of the middle lobe open behind the crest; at the forepart of the crest, below its summit, is a median elevation, the colliculus seminalis, upon or within the margins of which are the orifices of the prostatic utricle and the slit-like openings of the ejaculatory ducts[MP]
The conspicuous longitudinal fold of mucosa on the posterior wall of the female urethra[MP]
A transient developing limb structure that develops from the limb bud; it is a dorsoventral flattening of the limb bud structure and develops into the foot plate
A membranous urethra of male or female that is part of a female urethra.
the shortest, least dilatable, and, with the exception of the external orifice, the narrowest part of the male urethral canal located in the deep perineal pouch and lined by pseudostratified columnar epithelium; it extends downward and forward, with a slight anterior concavity, between the apex of the prostate and the bulb of the urethra, perforating the urogenital diaphragm below and behind the pubic symphysis; the membranous portion of the urethra is completely surrounded by the fibers of the sphincter urethrae membranaceae; on either side near its termination are the bulbourethral glands
The slit-like opening of either ureter into the bladder; normally, the two ureteral orifices are placed at the posterolateral angles of the urinary bladder trigone while the internal urethral orifice is placed at its anteroinferior angle (apex); wide gaping usually indicates vesicoureteral reflux
Caudally blind-ending cutaneous pouch lined with skin that occupies the nasoincisive notch. It's ventral and medial walls is formed by the alar fold. It's lateral wall is formed by the external nares and it's dorsal wall is formed by the straight fold. Lined by pigmented predominantly hairless skin. It has an external opening located on the dorsolateral aspect of the "true nostril". When the horse is exercising, obliteration of the nasal diverticulum greatly widens the nostrils increasing air intake[MURDOCH].
A fold of skin at the caudal border of the auricle.
The superficial lateral cervical lymph nodes are found in proximity to the external jugular vein.
The superficial anterior cervical lymph nodes are found in proximity to the anterior jugular vein.
superficial anterior cervical lymph node
The deep lateral cervical lymph nodes are found near the upper part of the internal jugular vein in the neck, lateral or posterior to the carotid sheath.
The deep anterior cervical lymph nodes are found near the middle cricothyroid ligament and the trachea.
One of five swellings formed during the development of the face
The point where the primary palate and both palatine shelves fuse.
Roof of the buccal cavity, formed from the fusion of vomer, pterygoid, parasphenoid, palatine, ectopterygoid.
Anatomical cluster that is the upper roof of the mouth that is underlain by bones such as the parasphenoid, vomer, metapterygoid, orbitosphenoid.[TAO]
Roof of the mouth lined with ciliated epithelium.[AAO]
The vaginal orifice is a median slit below and behind the opening of the urethra; its size varies inversely with that of the hymen.
The anterior ethmoidal artery, also anterior ethmoid artery is an artery of the head. Once branching from the ophthalmic artery, it accompanies the nasociliary nerve through the anterior ethmoidal canal to supply the anterior and middle ethmoidal cells, frontal sinus, and anterosuperior aspect of the lateral nasal wall[WP]
The posterior ethmoidal artery is an artery of the head. It is smaller than the anterior ethmoidal artery, branches off from the ophthalmic artery when it reaches the medial wall of the orbit.
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
The ascending cervical artery is a small branch which arises from the inferior thyroid artery as that vessel is passing behind the carotid sheath; it runs up on the anterior tubercles of the transverse processes of the cervical vertebrC& in the interval between the Scalenus anterior and Longus capitis. To the muscles of the neck it gives twigs which anastomose with branches of the vertebral, and it sends one or two spinal branches into the vertebral canal through the intervertebral foramina to be distributed to the medulla spinalis and its membranes, and to the bodies of the vertebrC&, in the same manner as the spinal branches from the vertebral. It anastomoses with the ascending pharyngeal and occipital arteries.
The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery.
Unclear if MA class belongs here or in parent
descending branch of the transverse cervical
Corpora allata with Corpora cardiaca form the retrocerebral complex, a neurosecretory organ.
The caudal, swollen portion of the gubernaculum.
In rodents, during inguinoscrotal descent the gubernaculum regresses and the bulb prolapses, forming the vaginal process[ISBN-10:0123971756]
Hrabovszky et al propose the bulb is the growing end of the elongating gubernaculum, analogous to the growth of a limb bud[PMID:11997885]
small saliences on the ridge of the glans of the male genital organs.
Keratinized structures along the glans and/or shaft of their penis that may be involved in sexual selection.
Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin.
epithelium stratificatum squamosum cornificatum
keratinized stratified squamous epithelium
The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals.
The mesosalpinx is part of the lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine tube to the level of the ovary.
A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis.
A pouch formed by the mesosalpinx and the mesovarium that encloses the infundibulum of the uterine tube and the ovary
Ovaries of some animals are surrounded by a thin membranous sac, the bursa, and are isolated from the peritoneal cavity. The bursa is continuous with the orifice of the oviduct. The bursa is not continuous in other mammals (eg., farm animals and human beings); ovaries of these species can be exposed within the abdomen, and thus ectopic pregnancy is possible[http://www.uwyo.edu/wjm/repro/femanat.htm]
A fluid-filled sac that lies between the navicular bone and the deep digital flexor muscle
A navicular bursa that is part of a manus.
A zone of skin that is part of the area surrounding the anus.
The cauda equina is a structure within the lower end of the spinal column of most vertebrates, that consists of nerve roots and rootlets from above. The space in which the cerebrospinal fluid is present is actually an extension of the subarachnoid space.
A navicular bursa that is part of a pes.
A gland whose discharged secretion contains entire secreting cells.
thin, pigmented, keratinised, hairless epidermis covering subcutaneous, collagenous, and adipose tissue.
A thick spongy structure at the base of the autopod, centred over the flexor surfaces of the distal interphalangeal joints.
An autopod pad found in the carpal region of a manus. Used for additional traction when stopping or descending a slope in digitigrade species.
A anatomical space that is enclosed by a urachus.
Extracellular matrix secreted by intraglomerular mesangial cells
Skeletal subdivision consisting of all the skeletal elements in a single fin.
The segment of the autopod that is distal to the metapodial region and consists of the digits.
class refers to an entire limb segment, not just the bones
The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers).
The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes).
A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.
A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton.
A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton.
A bone element that is part of a jaw region.
A epithelium that is part of a thyroid follicle.
portion of substance contained within the thyroid follicle lumen. Contains prohormone thyroglobulin.
A muscle layer that is part of an intestine.
longitudinal muscle layer of muscular coat
A nerve plexus that is part of a sympathetic nervous system.
The subserous part of the enteric plexus of autonomic nerves
A layer of tissue between the muscularis and serosa.
A muscular coat that is part of a jejunum.
A muscular coat that is part of a urinary bladder.
A circular muscle layer of muscular coat that is part of a large intestine smooth muscle.
circular muscle layer of segment of large intestine
large intestine smooth muscle circular layer
A longitudinal muscle layer of muscular coat that is part of a large intestine smooth muscle.
longitudinal muscle layer of zone of large intestine
large intestine smooth muscle longitudinal layer
A circular muscle layer of muscular coat that is part of a small intestine smooth muscle.
circular layer of small intestine muscularis propria
circular muscle layer of small intestine
short pitch helicoidal muscle layer of small intestine
stratum circulare (tunica muscularis)(intestinum tenue)
stratum helicoidale brevis gradus tunicae muscularis intestini tenuis
small intestine smooth muscle circular layer
A longitudinal muscle layer of muscular coat that is part of a small intestine smooth muscle.
long pitch helicoidal muscle layer of small intestine
longitudinal layer of small intestine muscularis propria
longitudinal muscle coat of small intestine
longitudinal muscle layer of small intestine
stratum helicoidale longi gradus tunicae muscularis intestini tenuis
stratum longitudinale (tunica muscularis) (intestinum tenue)
small intestine smooth muscle longitudinal layer
respiratory system arterial smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
The taeniae coli (also teniae coli) are three separate longitudinal ribbons of smooth muscle on the outside of the ascending, transverse, descending and sigmoid colons. They are visible, and can be seen just below the serosa or fibrosa. They are the Mesocolic, Free and Omental Coli. The teniae coli contracts length wise to produce the haustra, the bulges in the colon. The bands converge at the root of the vermiform appendix and the rectum. These bands correspond to the outer layer of the muscularis externa, in other portions of the digestive tract.
longitudinal band of large intestine muscularis
Most proximal cloacal compartment, into which the large intestine empties[Kardong]
Cloacal compartment into which the urogenital system empties[Kardong]
This is where the urates collect. In the hen the oviduct opens into this compartment.
Nutritional fluid secreted by the crop in some species[Kardong]
A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]
FMA class represents an individual microvillus.
The microvilli-covered surface of simple cuboidal epithelium and simple columnar epithelium cells found in certain locations of the body. Found in small intestine and kidney
A brush border layer that is part of a intestine.
brush border microvillus later of intestine
A brush border layer that is part of a proximal convoluted tubule.
Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
A anatomical line that adjacent_to a epithelium and adjacent_to a mesenchyme.
A blastema that is part of a regenerating fin/limb.
A blastema that is part of a distal segment of digit.
A endothelium that is part of a peritubular capillary.
The passage of communication, or foramen, between the general cavity (of the abdomen), and the omental bursa.
A single row of large ventral scales in snakes that aid locomotion.
retained pelvic vestiges found in birds. They are generally used in courtship and are more pronounced in males than females.
Obsoleted as lacks support in literature
A horny sheath covering the lower leg of some birds.
The Corpuscles of Herbst or Herbst corpuscles are a nerve-ending similar to the Pacinian corpuscle, in the mucous membrane of the tongue, in pits on the beak and in other parts of the bodies of birds. It differs from the Pacinian corpuscle in being smaller, in its capsules being more closely approximated, and in that the axis-cylinder in the central clear space is coated with a continuous row of nuclei. In many wading birds, a large number of Herbst corpuscles are found embedded in pits on the mandibles that are believed to enable birds to sense prey under wet sand or soil.
A sensory receptor that responds to mechanical pressure or distortion.
Normally there are four main types in glabrous skin: Pacinian corpuscles, Meissner's corpuscles, Merkel's discs, and Ruffini endings. There are also mechanoreceptors in hairy skin, and the hair cells in the cochlea are the most sensitive mechanoreceptors, transducing air pressure waves into nerve signals sent to the brain. In the periodontal ligament, there are some mechanoreceptors, which allow the jaw to relax when biting down on hard objects; the mesencephalic nucleus is responsible for this reflex
Meissner's corpuscles (or tactile corpuscles) are a type of mechanoreceptor. They are a type of nerve ending in the skin that is responsible for sensitivity to light touch. In particular, they have highest sensitivity (lowest threshold) when sensing vibrations lower than 50 Hertz. They are rapidly adaptive receptors.
tactile corpuscles of wagner and meissner
A sensory nerve ending that responds to a stimulus in the internal or external environment of an organism. In response to stimuli the sensory receptor initiates sensory transduction by creating graded potentials or action potentials in the same cell or in an adjacent one..
Specialized terminations of peripheral neurons. Nerve endings include NEUROEFFECTOR JUNCTION(s) by which neurons activate target organs and sensory receptors (see RECEPTORS, SENSORY) which transduce information from the various sensory modalities and send it centrally in the nervous system. Presynaptic nerve endings are PRESYNAPTIC TERMINALS.
this class and subclasses may be ceded to GO
mechanoreceptors found in the skin and mucosa of vertebrates that provide touch information to the brain. The information they provide are those regarding pressure and texture. Each ending consists of a Merkel cell in close apposition with an enlarged nerve terminal
In mammals, Merkel nerve endings have a wide distribution. Merkel nerve endings are found in the basal layer of glabrous and hairy skin, in hair follicles, and in oral and anal mucosa. In humans, Merkel cells (along with Meissner's corpuscles) occur in the superficial skin layers, and are found clustered beneath the ridges of the fingertips that make up fingerprints. In hairy skin, Merkel nerve endings are clustered into specialized epithelial structures called 'touch domes' or 'hair disks'. (Some other types of mechanoreceptors, such as Pacinian corpuscles and Ruffini endings, are found primarily in subcutaneous tissue.) Merkel receptors are also located in the mammary glands. Wherever they are found, the epithelium is arranged to optimize the transfer of pressure to the ending.
The Ruffini ending or Ruffini corpuscle is a class of slowly adapting mechanoreceptor which in humans is thought to exist only in the glabrous dermis and subcutaneous tissue[WP].
MP says subcutaneous tissue of digits; NCITA says hypodermis
highly vascular skin called velvet that covers the antler whilst it grows, supplying oxygen and nutrients to the growing bone.
Most distal cloacal compartment; function is copulation and in some species develops a penis[Kardong]
For most birds this is where the phallus is located, but male parrots do not have a phallus. The Bursa of Fabricius is located here.
A anatomical space that is enclosed by a cloaca.
the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/
The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives.
A anatomical space that is enclosed by a terminal part of digestive tract.
includes the cloacal lumen, in species where this is present
lumen of terminal part of digestive tract
An anatomical space with no opening to another space or to the exterior.
Tooth-like structure that typically forms a ring surrounding the anus of some Holothuriidae
the terminal papillae superficially resemble the ‘anal teeth’ of non-apodid holothurians.
Ligament extending between the liver and stomach
The hepatoduodenal ligament is the portion of the lesser omentum extending between the porta hepatis of the liver and the superior part of the duodenum.
Small tentacle-like structure surrounding the mouth; they act as sensory devices and as a filter for the water passing into the body
this class groups a chordate (branchiostome) and lophotrochozoan (brachiopod) structure; these should probably be split
A ventral evagination extending anteriorly in the mid-portion of the intestine in Amphioxi.
may be analagous to liver, Romer says not homologous
The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle.
skeleton of anterior limb/fin and girdle
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
skeleton of posterior limb/fin and girdle
The posterior region of the neck, including the suboccipital region.
A mucosa that is part of a cloaca [Automatically generated definition].
A submucosa that is part of a cloaca [Automatically generated definition].
A serous membrane that is part of a cloaca [Automatically generated definition].
A muscular coat that is part of a cloaca.
A sphincter muscle that is part of a vagina.
A muscular coat that is part of a duodenum.
A muscular coat that is part of a colon.
A muscular coat that is part of a anal canal.
A muscularis mucosa that is part of a duodenum.
lamina muscularis of duodenal mucous membrane
A muscularis mucosa that is part of a rectum.
lamina muscularis of rectal mucous membrane
A serous membrane that is part of a vermiform appendix.
visceral peritoneum of vermiform appendix
A serous membrane that is part of a fallopian tube.
A serous membrane that is part of a fundus of stomach.
visceral peritoneum of fundus of stomach
A adventitia that is part of a esophagus.
The superficial-most muscle of the anterior surface of the arm is the epitrochlearis. It has no homolog in humans.
A smooth muscle tissue that is part of a umbilical cord.
A muscle organ that is part of a Aristotle's lantern.
The vestimentum is a muscle that the tubeworm uses to anchro itself in the tube. Generates new tube material.
Vascularized tip of their free end of a tubeworm which is an organ for exchanging compounds with the environment.
An organ of dark green-brown spongy tissue in a tubeworm which is a host to symbiotic microbes
A specialised organ found in deep-sea tube worms populating hydrothermal vent environments that is colonised by chemosynthetic bacteria which supply the host worm with organic compounds. The term may be applied to similar organs in other worms[ENVO:01000165].
Organ at the distal end of a tubeworm. Helps anchor the tubeworm
Tube consists of chitin proteoglycan/protein complex
The ampulla is the second portion of the uterine tube. It is an intermediate dilated portion, which curves over the ovary. It is the most common site of human fertilization. The word ampulla is from the Latin for flask.
One of a pair of thin sheets of smooth muscle inserting on the rectum, having a tendinous origin largely on sacral vertebrae.
A anatomical junction that connects a stomach and connects a duodenum.
A mucosa that is part of a gastroduodenal junction.
The subdivision of the digestive tract that consists of the colon and the rectum.
A bony protuberance sometimes found on the hard palate at the junction of the intermaxillary suture and the transverse palatine suture.
In accordance with the N. A. 'Torus palatinus' denotes a median low ridge on the oral surface of the Palatum osseum. Crista palatina, however, refers in the N. A. to a transverse crest, which is present among domestic mammals only occasionally in the pig. See Os palatinum.[NOMINA ANATOMICA VETERINARIA (2005)]
A depression on the ventral side of the femur, at the knee joint, between the condyles.
A roughly triangular flap of skin on the wing of a bird or pterosaur which fills the space bounded by the humerus and ulna.
The rattle is composed of a series of hollow, interlocked segments made of keratin, which are created by modifying the scales that cover the tip of the tail.
An extension of the frontal sinus into the horn
BTO class may refer to invertebrate gland
Solutions or mixtures of toxic and nontoxic substances elaborated by snake (Ophidia) salivary glands for the purpose of killing prey or disabling predators and delivered by grooved or hollow fangs. They usually contain enzymes, toxins, and other factors.
A fang that is used to inject venom into prey, through either a tube or a groove
Venoms from snakes of the family Elapidae, including cobras, kraits, mambas, coral, tiger, and Australian snakes. The venoms contain polypeptide toxins of various kinds, cytolytic, hemolytic, and neurotoxic factors, but fewer enzymes than viper or crotalid venoms. Many of the toxins have been characterized.
Venoms of sea snakes, Hydrophiinae, found around Pacific islands. The venoms contain fewer enzymes and more neuro- or myotoxins than land snakes. The neurotoxic proteins are similar to elapid small, short, or type I neurotoxins, some of which have been characterized.
Venoms from snakes of the viperid family. They tend to be less toxic than elapid or hydrophid venoms and act mainly on the vascular system, interfering with coagulation and capillary membrane integrity and are highly cytotoxic. They contain large amounts of several enzymes, other factors, and some toxins.
Bone formed from the fusion of angular and surangular bones. Found in snakes
A prominent compressor muscle found in poisonous snakes that originates in the lower jaw, sweeps around the venom gland, and inserted on the gland's surface. The muscles acts to squeeze the gland and release venom.
only found in crotaline snakes, and has a spotty distribution within that group
A depression or fissure in the surface of the brain. It surrounds the gyri, creating the characteristic appearance of the brain in humans and other large mammals.
Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)
A lymphoid organ found in various mammals and some birds.
Hemal nodes are characterized by the presence of large numbers of erythrocytes. Lymph nodes (see below) and hemal nodes share some similarities of structure, but really are fundamentally different organs both qualitatively and quantitatively. Both lymph and hemal nodes contain diffuse lymphatic tissue, and in most cases have nodular tissue in the form of germinal centers, as well. Like the lymph node, the hemal node has a cortex and a medulla, and germinal centers are frequently seen. There's a distinct capsule, and hemal nodes are served at the hilus by an afferent arteriole. [http://www.vetmed.vt.edu/education/curriculum/vm8054/labs/lab13/lab13.htm]
A posterior cardinal vein that is in_the_left_side_of a multicellular organism.
A subcardinal vein that is in_the_left_side_of a multicellular organism.
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
The part of the venous system that drains the lungs[Kardong]
Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung.
Just before each crus of the penis meets its fellow it presents a slight enlargement, named by Kobelt the bulb of the corpus spongiosum penis. It is homologous to the vestibular bulbs in females.
Aggregations of erectile tissue that are an internal part of the clitoris. They can also be found throughout the vestibule: next to the clitoral body, clitoral crura, urethra, urethral sponge, and vagina.
Cavernous organ, located in labium minus . Examples: There iare only two bulbs of vestibule, the right and the left.[FMA]
One of the small straight arteries of the red pulp of the spleen; a branch of the spleen central artery that supplies the red pulp[WP,modified]
A phrenic artery that arises from the lower part of the thoracic aorta and is distributed to the posterior part of the upper surface of the diaphragm, and anastomoses with the musculophrenic and pericardiacophrenic arteries.
The interdental plate refers to the bone-filled mesial-distal region between the teeth
In paleobiology, the presence or absence of the interdental plate can determine the place of an animal in the evolutionary scale, and paleontologists use the interdental plate when trying to classify a new specimen. Thecodont reptiles and theropod dinosaur fossils have an interdental plate, whereas acrodont reptiles such as Sphenodontia do not.[3] Its presence in Archaeopteryx, an extinct avian, resulted in the proposal of the dinosaur-bird connection
Either the superficial or deep external pudendal arteries
The coronary ligament of the liver refers to parts of the peritoneal reflections that hold the liver to the inferior surface of the diaphragm.
A nonskeletal ligament that is part of a liver.
Any vein within the general circulation that transports blood back to the right atrium of the heart.
divided in medial gastrocnemius vein (vena medialis gastrocnemii), lateral gastrocnemius vein (vena lateralis gastrocnemii), and intergemellar vein (Vena intergemellaris), the vein ascending between the two heads of the gastrocnemius[http://www.veinsurg.com/fr/biblio/echodoppler/echodoppler_11.php]
The term genicular venous plexus (plexus venosus genicularis) should replace the term genicular veins. At the knee, deep veins do not correspond exactly to the branches of the popliteal artery (articular arteries). They are arranged in a complex plexus of interconnecting veins.[http://www.veinsurg.com/fr/biblio/echodoppler/echodoppler_11.php]
gives rise to midbrain vesicle which gives rise to cerebral aqueduct
TODO - resolve space vs structure inconsistency; consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle'
One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions.
A temporary opening between the developing ventricles of the heart. The ventricles arise as a single cavity is divided by the developing interventricular septum. Before the septum closes completely, the remaining opening between the two ventricles is termed the interventricular foramen.
Phenotype notes: In some individuals, the foramen fails to close, leading to an interventricular septal defect known as a patent interventricular foramen
Small protrusions of the arachnoid mater into vascular sinuses, acting as one-way pressure-sensitive valves.
Arachnoid granulations (or arachnoid villi) are small protrusions of the arachnoid (the thin second layer covering the brain) through the dura mater (the thick outer layer). They protrude into the venous sinuses of the brain, and allow cerebrospinal fluid (CSF) to exit the brain, and enter the blood stream. Largest granulations lie along the superior sagittal sinus, a large venous space running from front to back along the centre of the head (on the inside of the skull). They are, however, present along other dural sinuses as well. Smaller granulations are called villi, large calcified ones are referred to as pacchionian bodies[Wikipedia:Arachnoid_granulation].
1st arch maxillary-mandibular groove ectoderm
A gland that is part of a foregut-midgut junction.
A telencephalic ventricle that is in_the_left_side_of a telencephalon.
A telencephalic ventricle that is in_the_right_side_of a telencephalon.
A depression in front of the epiglottis, in which food is temporarily gathered as the animal chews.
Region of surface of viscerocranial mucosa, which is a depression located between the median and lateral glosso-epiglottic folds. Examples: There are only two instances, right and left epiglottic valleculas[FMA:55037].
On the upper surface of the cerebellum the vermis is elevated above the level of the hemispheres, but on the under surface it is sunk almost out of sight in the bottom of a deep depression between them; this depression is called the vallecula of the cerebellum, and lodges the posterior part of the medulla oblongata.
Laryngeal ligament that connects the cricoid cartilage to the pharynx[WP,modified]
Laryngeal ligament that connects the epiglottis to the thyroid cartilage[WP,modified]
The vestibular fold is a fibroelastic band which passes from the ventral margin of the cuneiform cartilage to the cranial dorsal surface of the thyroid cartilage. It forms the support for the free edge of the vestibular fold.
Laryngeal ligament that connects the cricoid and arytenoid cartilages[WP,modified]
This attaches the caudal border of the thyroid cartilage to the ventral arch of the cricoid cartilage. Its sheetlike ventral portion is sometimes referred to as the cricothyroid membrane. Being elastic, it 'balances' movement at the hinge-like cricothyroid joint and determines the resting position of the larynx when the muscles are relaxed[MURDOCH]. The cricothyroid ligament is the larger part of the laryngeal membrane, continuing inferiorly as a median or anterior part and twin lateral ligaments. The median cricothyroid ligament is a flat band of white tissue joining the cricoid and thyroid cartilages, while the lateral cricothyroid ligament is also known as the cricothyroid membrane (also called conus elasticus).
The cricotracheal ligament connects the cricoid cartilage with the first ring of the trachea[WP]. The caudal border of the cricoid cartilage is joined to the first ring of the trachea by this ligament. It is an extrinsic laryngeal ligament. It resembles the fibrous membrane which connects the cartilaginous rings of the trachea to each other.
A wavy crest externally on the tympanic bone of cetaceans.
An air sac opening into the passage of the blowhole that is hypothesized to be involved in echolocation
requires review w.r.t location in physeter vs other odontocetes
When the lips snap together during click production, vibrations in the dorsal bursae are likely produced ISBM10:0120885522. Large and cornified in sperm whales
right posterior dorsal bursa may be homologous to spermaceti organ
Likely involved in regulating air movement in perhaps whistle production
A structure consisting of a pair of anterior and posterior dorsal bursae in which a pair of phonic lips are embedded, along with the bursal cartilage and a blowhole ligament
all odontocetes except sperm whales posses two bilaterally placed MLDB complexes, placed just below the floor of the vestibular sac
Entotympanics are independent elements present in the auditory bullae of various eutherians
The outer layer of the ovary, composed of cellular connective tissue which contains the ovarian follicles
The medulla of ovary (or Zona vasculosa of Waldeyer) is a highly vascular stroma in the center of the ovary. It forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves. This stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter: it does not contain any ovarian follicles.
composed of loose connective tissue that contains blood vessels, lymph vessels and nerves
An epithelium that is characterized by incomplete keratinization of the cells in the stratum corneum. The cells are flattened and composed primarily of packed tonofilaments. However, the cells may retain remnants of nuclei and other organelles
A keratinized epithelium in which the cells of the stratum corneum become very flat, loose their nuclei and cytoplasmic organelles and are now composed of densely packed tonofilaments cemented by filaggrin
A parakeratinized epithelium that is part of a gingiva.
A casing spun of silk by many moth caterpillars, and numerous other holometabolous insect larvae as a protective covering for the pupa[WP].
analagous to a puparium in other insects
Set of nerve fibers conducting impulses from olfactory receptors to the cerebral cortex. It includes the olfactory nerve; olfactory bulb; olfactory tract, olfactory tubercle, anterior perforated substance, and olfactory cortex. The term rhinencephalon is restricted to structures in the CNS receiving fibers from the olfactory bulb.
The hypogastrium (or hypogastric region, or pubic region) is an area of the human abdomen located below the navel.
One of a pair of bones running antero-laterally from the centre of the pubis in marsupials and some other mammals
Epipubic bones are a pair of bones projecting forward from the pelvic bones of modern marsupials and of some fossil mammals: multituberculates, monotremes, and even basal eutherians (the ancestors of placental mammals). In modern marsupials the epipubic bones are often called 'marsupial bones' because they support the mother's pouch ('marsupium' is Latin for 'pouch'), but their presence on other groups of mammals indicates that this was not their original function, which some researchers think was to assist locomotion by supporting some of the muscles that flex the thigh. The epipubic bones were first described in 1698 but their functions have remained unresolved. It has been suggested that they form part of a kinetic linkage stretching from the femur on one side to the ribs on the opposite side. This linkage is formed by a series of muscles: each epipubic bone is connected to the femur by the pectineus muscle, and to the ribs and vertebrae by the pyramidalis, rectus abdominis, and external and internal obliques. According to this hypothesis, the epipubic bones act as levers to stiffen the trunk during locomotion[Wikipedia:Epipubic_bone].
A fleshy appendage ringing the snout of a Star-nosed mole.
A canal through the medial epicondyle at the distal end of the vertebrate humerus, usually traversed by the median nerve and brachial artery.
It is often present in primitive placentals, such as the enigmatic Madagascan Plesiorycteropus. In most Neotominae and all Tylomyinae among cricetid rodents, it is located above the medial epicondyle of the humerus, but it is absent in all Sigmodontinae and Arvicolinae and this trait has been suggested as a synapomorphy for the former subfamily.[WP]
Primitive amniote feature found in primitive reptil-like amphibians (Romeer) [http://www.jstor.org/discover/10.2307/2422468]
An olfactory ganglion at the entrance of the nose of mammals that is involved in the detection of alarm pheromones and cold temperatures.
A specialized sudoriferous gland (sweat glands) located subcutaneously in the external auditory canal.
Ceruminous glands are simple, coiled, tubular glands made up of an inner secretory layer of cells and an outer myoepithelial layer of cells. The glands drain into larger ducts, which then drain into the guard hairs that reside in the external auditory canal. Here they produce cerumen, or earwax, by mixing their secretion with sebum and dead epidermal cells
A bodily secretion that is produced by a gland of anal sac.
Ossicones are horn-like protuberances on the heads of giraffes, male okapis, and their extinct relatives, such as Sivatherium, and the climacoceratids, such as Climacoceras. Only giraffids have true ossicones (as opposed to horns or antlers). The base that a deer's antlers grow from is very similar to ossicones. Ossicones are similar to the horns of antelopes and cattle, save that they are derived from ossified cartilage, and that the ossicones remain covered in skin and fur, rather than horn. Antlers (such as on deer) are derived from bone tissue: when mature, the skin and fur covering of the antlers, termed 'velvet,' is sloughed and scraped off to expose the bone of the antlers.
A large pendulous organ consisting of two or more mammary glands enclosed in a common envelope and each provided with a single nipple.
An udder is an organ formed of the mammary glands of female quadruped mammals, especially ruminants such as cattle, goats, sheep and deer. The udder is a single mass hanging beneath the animal, consisting of pairs of mammary glands. In cattle there are normally two pairs, in sheep, goats and deer there is one pair, and in some animals such as pigs there are many pairs. Udder care and hygiene in cows is important in milking, aiding uninterrupted and untainted milk production, and preventing mastitis. Products exist to soothe the chapped skin of the udder. This helps prevent bacterial infection, and reduces irritation during milking by the cups, and so the cow is less likely to kick the cups off[Wikipedia:Udder].
In rodent anatomy, the zygomatic plate is a bony plate derived from the flattened front part of the zygomatic arch (cheekbone). At the back, it connects to the front (maxillary) root of the zygomatic arch, and at the top it is connected to the rest of the skull via the antorbital bridge. It is part of the maxillary bone, or upper jaw, which also contains the upper cheekteeth. Primitively, rodents have a nearly horizontal zygomatic plate. In association with specializations in zygomasseteric system, several distinct morphologies have developed across the order. The term is also used for an analogous structure in some South American typotheres, including Pseudotypotherium and Medistylus.
A rete mirabile (Latin for 'wonderful net'; plural retia mirabilia) is a complex of arteries and veins lying very close to each other, found in some vertebrates. The rete mirabile utilizes countercurrent blood flow within the net (blood flowing in opposite directions. ) It exchanges heat, ions, or gases between vessel walls so that the two bloodstreams within the rete maintain a gradient with respect to temperature, or concentration of gases or solutes.
The parotoid gland (alternatively, paratoid gland) is an external skin gland on the back, neck, and shoulder of toads and some frogs and salamanders. It secretes a milky alkaloid substance to deter predators. The substance produced acts as a neurotoxin. Parotoid glands are sometimes said to be wart-like in appearance, though warts are abnormal growths caused by viral infections while parotoid glands are normal, healthy parts of the animals that bear them. The vague similarity in appearance, however, is the reason behind the mistaken belief that touching a toad causes warts.
A hole with that connects the left and right aorta in animals of the order Crocodilia.
Crocodilians have a completely separated ventricle with deoxygenated blood from the body, or systemic circulation, in the right ventricle and oxygenated blood from the lungs, or pulmonary circulation, in the left ventricle, as in birds and mammals. Two vessels, the left aorta and the pulmonary artery, exit the right ventricle. Blood from the right ventricle goes to the lungs through the pulmonary artery, as in mammals and birds. However, when a unique active valve leading to the pulmonary artery contracts, pressure in the right ventricle can increase and blood can leave the right ventricle, enter the left aortic arch, and therefore bypass the pulmonary circulation. The foramen of panizza connects the left and right aorta. Deoxygenated blood from the right ventricle, sitting in the left aorta, can flow into the right aorta through the foramen of panizza. When the heart is relaxed, some oxygenated blood from the left ventricle, sitting in the right aorta, can flow into the left aorta across the foramen of panizza. However, some species of Crocodilians have regulatory sphincters that prevent unwanted flow of blood through the foramen of panizza during non-diving
The caudofemoralis (from the latin cauda, tail and femur, thighbone) is a muscle found in the pelvic limb of mostly all animals possessing a tail, since it is a synapomorphy appeared on the Archosauria clade. It is thus found in felids (cats) and Mustela ('Weasels'), but also on crocodiles and birds.
The Caudofemoralis acts to flex the tail laterally to its respective side when the pelvic limb is bearing weight. When the pelvic limb is lifted off the ground, contraction of the Caudofemoralis causes the limb to abduct and the shank to extend by extending the hip joint (acetabulofemoral or coxofemoral joint)
Otic notches are invagination in the posterior margin of the skull roof, one behind each orbit. Such notches are found in labyrinthodonts and some of their immediate ancestors, but not their reptilian descendants. The presence or absence of the otic notches is one of the traits used to separate the amniotes from the amphibian grade tetrapods. The notches have been interpreted as part of an auditory structure, and are often shown holding a tympanum similar to those seen in modern anurans. Analysis of the columella (the stapes in amphibians and reptiles) of labyrinthodonts however indicate it did not function in transmitting low energy vibrations, thus rendering them effectively deaf to airborne sound. The otic notch instead functioned as a spiracle, at least in the early forms.
In contrast to tubular glands, in the second main variety of gland, the secretory portion is enlarged and the lumen variously increased in size. These are termed alveolar glands (or saccular glands, or acinar glands, or acinous glands). Some sources draw a clear distinction between acinar and alveolar glands, based upon the shape of the lumen. A further complication in the case of the alveolar glands may occur in the form of still smaller saccular diverticuli growing out from the main sacculi. These are termed alveoli. The term 'tubulo-alveolar' (or 'tubulo-acinar', or 'compound tubulo-acinar', or 'compound tubulo-alveolar') is used to describe glands that start out as branched tubular, and branch further to terminate in alveoli. This type of gland is found in the salivary glands, esophagus, and mammary glands. The term 'racemose gland' is used to describe a 'compound alveolar gland' or 'compound acinar gland'.
Ciaccio's glands are small tubular accessory lacrimal glands (glandulae lacrimales accessoriae) found in the lacrimal caruncle of the eyelid. They are located in the upper border of the tarsus, approximately in the middle between the extremities of the tarsal glands. Sometimes they are situated slightly above the tarsus. There are usually 2 to 5 of these glands in the upper eyelid, and their function is to produce tears which are secreted onto the surface of the conjunctiva. They are named after Italian anatomist Giuseppe Vincenzo Ciaccio (1824b1901), who described these glands in 1874. They are sometimes called Wolfring's glands after Polish ophthalmologist Emilj von Wolfring (1832-1906), who described them during the same time period as did Ciaccio. Another type of accessory lacrimal gland are Krause's glands, which are smaller, more numerous than Ciaccio's glands and are found along the superior and inferior fornices of the conjunctival sac.
Serous gland with distended lumen. It includes the gland of Krause in the lacrimal sac and the gland of Wolfring on the inner surface of the upper eyelid. (NCI)
may be re-classified as a sibling on lacrimal gland
Crypts of Henle are microscopic pockets found in scattered sections of the conjunctiva around the eyeball. They are responsible for secreting mucin, a proteinous substance that makes up the inner layer of tears. It coats the cornea to provide a hydrophilic layer that allows for even distribution of the tear film. The layer of mucin allows tears to glide evenly across the eye’s surface[WP].
Glands of Moll, also known as ciliary glands, are modified apocrine sweat glands that are found on the margin of the eyelid. They are next to the base of the eyelashes, and anterior to the Meibomian glands within the distal eyelid margin. These glands are relatively large and tubular-shaped. The glands of Moll are named after Dutch oculist Jacob Anton Moll (1832–1914). Glands of Moll empty into the adjacent lashes. Glands of Moll and Zeis secrete lipid that adds to the superficial layer of the tear film, retarding evaporation. The glands of Moll are prone to infection and blockage of its duct with sebum and cell debris. Blockage of the gland's duct causes swelling which can manifest itself as a stye.
Any gland that is part of an eyelid. This includes sebaceous glands (Zeis gland, tarsal gland) and sweat glands (Moll's gland).
A gland producing tears in a third eyelid in the corner of each eye.
This gland is distinct from the other medial ocular gland, the Harderian gland, and is typified by clusters of glandular tissue within the nictitating membrane
superficial gland of the nictitating membrane
Disease notes: Prolapse of the Nicititans Gland is also known as Cherry Eye
Any of the sebaceous glands that are in the eyelid. Examples: gland of Zeis (services eyelashes), gland of Meibom (tarsal gland - unconnected to eyelids).
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
A lateral nasal gland that removes sodium chloride from the bloodstream.
The gland's function is similar to that of the kidneys, though it is much more efficient at removing salt, allowing Penguins to survive without access to fresh water. Contrary to popular belief, the gland does not directly convert saltwater to freshwater. The term supraorbital refers to the area just above the eye socket (which is known as the orbit of the eye. ) Living in saltwater environments would naturally pose a large problem for penguins because the ingestion of saltwater would be detrimental to a penguin's health. Although penguins do not directly drink water, it is taken in when they engulf prey. As a result, saltwater enters their system and must be effectively excreted. The supraorbital gland has thus enabled the penguins' survival in such environments due to its water-filtering capability. The gland is located just above the eyes and surrounds a capillary in the head. This capillary constantly strains out the salt in the saltwater that a penguin takes in. Since the byproduct of the gland has roughly five times as much salt as would normally be found in the animal's fluids, the supraorbital gland is highly efficient. The penguin excretes the salt byproduct as a brine through its bill. Often, the fluid drips out, and this gives the appearance of a runny nose. However, the fluid may also be sneezed out. In the absence of saltwater, caused by captivity, the supraorbital gland will lie dormant as it has no other purpose. Having a dormant supraorbital gland does not negatively affect the health of a penguin
The violet gland or supracaudal gland is an important gland located on the upper surface of the tail of certain mammals, including European badgers and canids such as foxes, wolves the domestic dog, as well as the domestic cat. It is used for intra species signalling, scent marking, and contributes to the strong odor of foxes in particular.
The subdivision of the trunk that overlaps with the ventrum.
Subdivision of trunk which is demarcated from the back of trunk by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall and from the limbs by the inguinal folds; together with the back of trunk, it constitutes the trunk. Examples: There is only one trunk proper[FMA:25055].
The genital papilla is a part of female external genitalia not present in humans, which appears as a small, fleshy flab of tissue. The papilla covers the opening of the vagina.
A future glans that is part of a male genital tubercle.
A future glans that is part of a female genital tubercle.
In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week
The vaginal plate is a precursor to the inferior portion of the vagina. They form from sinovaginal bulbs.
solid evaginations of the UG sinus that develops into a vaginal plate that which will will eventually canalize to form the inferior portion of the vagina.
A epithelial tube that develops_from a Mullerian duct and is part of a male reproductive system.
degenerating mesonephric portion of male paramesonephric duct
A small collection of convoluted tubules, situated in front of the lower part of the cord above the head of the epididymis. These tubes are lined with columnar ciliated epithelium, and probably represent the remains of a part of the Wolffian body but are functionless and vestigial. The Wolffian body operates as a kidney (metanephros) in fishes and amphibians, but the corresponding tissue is co-opted to form parts of the male reproductive system in other classes of vertebrate. The paradidymis represents a remnant of an unused, atrophied part of the Wolffian body[WP,modified].
A collection of a few scattered rudimentary tubules child, situated in the broad ligament between the epoophoron and the uterus.
In connection with the fimbriae of the uterine tube, or with the broad ligament close to them, there are frequently one or more small pedunculated vesicles. These are termed the vesicular appendages of the epoophoron.
one of the small pedunculated structures attached to the uterine tubes near their fimbriated end; remnants of the mesonephric ducts[http://medical-dictionary.thefreedictionary.com/].
remnant in a female of the portion of the embryonic mesonephric duct that develops into the ductus deferens in males.
incompletely obliterated remnants of the vaginal process of the peritoneum remaining in the spermatic cord.
A patent pouch of peritoneum extending into the labia majora of women. It is analogous to the processus vaginalis in males. The pouch accompanies the gubernaculum during development of the urinary and reproductive organs, more specifically during the descent of the ovaries, and normally obliterates.
A diaphysis that is part of a fibula[Automatically generated definition].
The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula].
The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia].
A silver reflective layer in the outer choroid, adjacent to the sclera, frequently present in fish larvae but not as frequent in adults. In species known to have a stratum argenteum as adults, like the toadfish (Toad- fishes), the tapetum lucidum is absent or vestigial and there is little choroidal melanin.
A gland that is part of a optic choroid.
Teleosts bear a body of capillary adjacent to the optic nerve called the choroidal gland. Though its function is not known, it is believed to be a supplemental oxygen carrier[http://en.wikipedia.org/wiki/Choroid#In_bony_fish].
a gland on the dorsal half of the fish eyeball[http://en.academic.ru/dic.nsf/en_ichthyology/2916/choroid]l
a layer of medium-diameter blood vessels of the choroid, a layer of the eye[Wikipedia:Sattler's_layer].
The asterion is the point on the skull corresponding to the posterior end of the parietomastoid suture.
The bregma is the anatomical point on the skull at which the coronal suture is intersected perpendicularly by the sagittal suture.
Anatomical cranial point where the coronal and sagittal suture lines intersect[FMA:264776].
The cranial cavity, or intracranial space, is the space formed inside the skull. The brain occupies the cranial cavity, which is lined by the meninges and which contains cerebrospinal fluid to cushion blows. Eight fused cranial bones together form the cranial cavity: the frontal, occipital, sphenoid and ethmoid bones, and two each of the parietal and temporal bones. The capacity of an adult human cranial cavity is 1,200-1,700 cm.
The crotaphion refers to two points on the skull at the tips of the greater wing of sphenoid bone. It is near the pterion.
The Epicranium is the medical term for the collection of structures covering the cranium. It consists of the muscles, aponeurosis, and skin.
Groove for Sigmoid Sinus is a groove in the posterior cranial fossa.
The infratemporal fossa is an irregularly shaped cavity, situated below and medial to the zygomatic arch. Boundaries defined by: anteriorly, by the infratemporal surface of the maxilla and the ridge which descends from its zygomatic process posteriorly, by the articular tubercle of the temporal and the spinal angularis of the sphenoid superiorly, by the greater wing of the sphenoid below the infratemporal crest, and by the under surface of the temporal squama, containing the foramen ovale, which transmits the mandibular branch of the trigeminal nerve, and the foramen spinosum, which transmits the middle meningeal artery inferiorly, by the medial pterygoid muscle attaching to the mandible medially, by the lateral pterygoid plate laterally, by the ramus of mandible, which contains the mandibular foramen, leading to the mandibular canal through which the inferior alveolar nerve passes. This also contains the lingula, a triangular piece of bone that overlies the mandibular foramen antero-medially. Finally, the mylohyoid groove descends obliquely transmitting the mylohyoid nerve the only motor branch of the anterior division of the trigeminal nerve.
The jugal point is the point at the anterior end of the upper border of the zygomatic arch where the masseteric and maxillary edges meet at an angle.
The occipital angle is rounded and corresponds with the point of meeting of the sagittal and lambdoidal sutures—a point which is termed the lambda (after the Greek letter of the same name); in the fetus this part of the skull is membranous, and is called the posterior fontanelle.
anatomical point connecting sagittal and lambdoidal sutures
The term obelion is applied to that point of the sagittal suture which is on a level with the parietal foramina.
A prominent bulge, or projection, of the occipital bone at the back of the skull[WP].
Occipital buns are important in scientific descriptions of classic Neanderthal crania. While common among many of mankind's ancestors, primarily robust relatives rather than gracile, the protrusion is relatively rare in modern Homo sapiens..
The ophryon is the point in the forehead just above the optic foramen, or eyesocket, and glabella.
The porion is the point on the human skull located at the upper margin of each ear canal (external auditory meatus, external acoustic meatus). It underlies the tragus. The anatomical landmark has significance in biological anthropology and craniometry.
The Postorbital Process marks the rear, upper edge of the eye socket and is a projection from the frontal bone.
The pterygomaxillary fissure is a fissure of the human skull. It is vertical, and descends at right angles from the medial end of the inferior orbital fissure; it is a triangular interval, formed by the divergence of the maxilla from the pterygoid process of the sphenoid. It connects the infratemporal with the pterygopalatine fossa, and transmits the terminal part of the maxillary artery. Alveolar branches of the maxillary nerve go from the pterygopalatine fossa to the infratemporal region via this fissure. In older texts, the pterygomaxillary fissure is sometimes called the pterygopalatine fissure.
A ridge of bone running lengthwise along the midline of the top of the skull of many mammalian and reptilian skulls and serves as an attachment site for the temporailis muscle[WP,modified].
Skulls of some dinosaur species, including tyrannosaurs, possessed well developed sagittal crests. Among mammals, dogs, cats, lions, and many other carnivores have sagittal crests, as do some leaf eaters, including tapirs and some apes. Sagittal crests are found in robust great apes, and some early hominins. Prominent sagittal crests are found among male gorillas and orangutans, and do occur but only rarely in male chimpanzees such as Bili Apes
The sagittal crest serves primarily for attachment of the temporalis muscle, which is one of the main chewing muscles
Compare with: AAO:0000384 parasagittal crest (UBERON:0013402)
The Sagittal keel (torus) is a thickening of bone on part or all of the midline of the frontal bone, or parietal bones where they meet along the sagittal suture, or on both bones..
Sagittal keels occur in Homo erectus and occasionally Homo heidelbergensis, where they probably served as an armour against shock to the roof of the skull, and as the attachment point for the temporalis muscles. Most Homo sapiens lost them likely as part of the general trend toward thinning of the cranial bones during the Pleistocene, to make room for larger brains. However there is a very small portion of modern humans who have this, but its function and etiology are unknown. Patrick Stewart of Star Trek and the martial artist Shi Yan Ming present good examples of modern humans with this feature.
A bony buttress on the inner surface of the foremost part of the ape mandible, functioning to reinforce the mandible.
The speno-maxillary fossa is a small triangular space situated at the angle of the junction of the spheno-maxillary and pterygo-maxillary fissures, and placed beneath the apex of the orbit. It is formed above by the under surface of the body of the sphenoid and by the orbital process of the palate bone.
The sphenopetrosal fissure (or sphenopetrosal suture) is the cranial suture between the sphenoid bone and the petrous portion of the temporal bone. It is in the middle cranial fossa.
The point where the upper temporal line cuts the coronal suture is named the stephanion.
The suprainiac fossa is an elliptic depression on the occiput above the superior nuchal line, or inion.
The Sylvian point is the point on the human skull nearest the Sylvian fissure and is located about 30 millimeters behind the Zygomatic process of frontal bone.
The temporal fossa is a shallow depression on the side of the skull bounded by the temporal lines and terminating below the level of the zygomatic arch.
The zygomasseteric system (or zygomasseteric structure) in rodents is the anatomical arrangement of the masseter muscle of the jaw and the zygomatic arch of the skull. The anteroposterior or propalinal (front-to-back) motion of the rodent jaw is enabled by an extension of the zygomatic arch and the division of the masseter into three distinct parts. The main types are described as protrogomorphous, sciuromorphous, hystricomorphous, and myomorphous.
obsoleted as it did not represent a structure
The Zygomatic Fossa is an irregularly shaped cavity, situated below and on the inner side of the zygoma; bounded, in front, by the zygomatic surface of the superior maxillary bone and the ridge which descends from its malar process; behind, by the posterior border of the external pterygoid plate and the eminentia articularis; above, by the pterygoid ridge on the outer surface of the great wing of the sphenoid and the under part of the squamous portion of the temporal; below by the alveolar border of the superior maxilla; internally, by the external pterygoid plate; and externally, by the zygomatic arch ramus of the lower jaw. It contains the lower part of the temporal, the External and Internal pterygoid muscles, the internal maxillary artery and vein, and inferior maxillary nerve and their branches. At its upper and inner part may be observed two fissures, the spheno-maxillary and pterygo-maxillary.
Near the middle of the occipital squama is the external occipital protuberance, and extending lateralward from it on either side is the superior nuchal line, and above this the faintly marked highest nuchal line. It is less pronounced in females. The inion is the highest point of the external occipital protuberance. a projection on the external surface of the squamous part of the occipital bone in the midline
The external occipital protuberance is a bony prominence occuring on the large area ventral to the external sagittal crest. It functions as the attachment site for the funicular part of the nuchal ligament[MURDOCH:734].
The retromolar space or retromolar gap is a space at the rear of a mandible, between the back of the last molar and the anterior edge of the ascending ramus where it crosses the alveolar margin.[WP]
Retromolar gap is found in some Neandertals because they had midfacial prognathism. This caused the lower toothrow to move forward, which led to the retromolar gap..
The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type.
The lower one third of the esophagus in which the muscle layer is composed of muscle cells predominantly of the smooth type.
The middle one third of the esophagus in which the muscle layer is composed of muscle cells of the striated and smooth types.
A serous salivary gland which resides adjacent to the moats surrounding the circumvallate papillae in the posterior one-third of the tongue, anterior to the terminal sulcus.
A hole at the top of a cetacean's head through which the animal breathes air
Baleen whales have two blowholes positioned in a V-shape while toothed whales have only one blowhole. The blowhole of a sperm whale, a toothed whale, is located left of centre in the frontal area of the snout, and is actually its left nostril, while the right nostril lacks an opening to the surface despite the fact that its nasal passage is otherwise well developed.
A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus.
In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil
A blood vessel endothelium that is part of a lung [Automatically generated definition].
An intestinal crypt that is located in the ileum.
An intestinal crypt that is located in the duodenum.
An intestinal crypt that is located in the jejunum.
An intestinal crypt that is located in the colon. The colonic crypts of Lieberkühn are straight and unbranched and lined largely with goblet cells.
An intestinal crypt that is located in the appendix.
The grooves in the outermost layer of skin on the palms of the hands and soles of the feet where sweat glands open.
The panniculus adiposus is the fatty layer of the subcutaneous tissues, superficial to a deeper vestigial layer of muscle, the panniculus carnosus. An example is the Fascia of Camper. Another example is the superficial cervical fascia[WP]
It includes structures that are considered fascia by some sources but not by others. Consider merging with subcutaneous adipose tissue
Superficial cervical fascia is a thin layer of subcutaneous connective tissue that lies between the dermis of the skin and the deep cervical fascia. It contains the platysma, cutaneous nerves, blood, and lymphatic vessels. It also contains a varying amount of fat, which is its distinguishing characteristic.
superficial layer of deep cervical fascia
It is considered by some to be a part of the Panniculus adiposus, and not true fascia[WP]
The deep cervical fascia (or fascia colli in older texts) lies under cover of the Platysma, and invests the neck; it also forms sheaths for the carotid vessels, and for the structures situated in front of the vertebral column. Its attachment to the hyoid bone prevents the formation of a dewlap. The investing portion of the fascia is attached behind to the ligamentum nuchC& and to the spinous process of the seventh cervical vertebra. The 'alar fascia' is a portion of deep cervical fascia.
The cervical fascia is fascia found in the region of the neck. It mainly refers to the deep cervical fascia. However, there are other cervical fascia: superficial cervical fascia prevertebral fascia
The prevertebral fascia (or prevertebral layer of cervical fascia) is a fascia in the neck.
lamina prevertebralis (fascia cervicalis)
prevertebral layer of deep cervical fascia
A modified strand of hair covered in a keratin coat, as found in porcupines and hedgehogs.
A keratin-coated spine that is tipped with a barb.
Porcupines' quills, or spines, take on various forms, depending on the species, but all are modified hairs coated with thick plates of keratin, and they are embedded in the skin musculature. Old World porcupines (Hystricidae) have quills embedded in clusters, whereas in New World porcupines (Erethizontidae), single quills are interspersed with bristles, underfur and hair.
A keratin-coated spine that is lacks a barbed end.
A fringe of muscle running along the periphery of the panniculus.
Hedgehogs roll into a ball via contraction of this muscle
vestibulo-cochlear VIII ganglion complex
glossopharyngeal-vagus preganglion complex
glossopharyngeal-vagus IX-X preganglion complex
glossopharyngeal-vagus IX-X ganglion complex
A sphincter muscle that is part of a cloaca.
the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938).
A mesenchyme that is part of a pharyngeal arch 5.
A caudal vertebra endochondral element that is composed primarily of a cartilage tissue.
coccygeal vertebral cartilage condensation group
A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
coccygeal vertebra pre-cartilage condensation
tail vertebral pre-cartilage condensation
caudal vertebra pre-cartilage condensation
A cervical vertebra endochondral element that is composed primarily of a cartilage tissue.
cervical vertebral cartilage condensation group
A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
cervical vertebra pre-cartilage condensation
A thoracic vertebra endochondral element that is composed primarily of a cartilage tissue.
thoracic vertebral cartilage condensation group
A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
thoracic vertebra pre-cartilage condensation
A lumbar vertebra endochondral element that is composed primarily of a cartilage tissue.
lumbar vertebral cartilage condensation group
A lumbar vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
lumbar vertebra pre-cartilage condensation
A long muscle found in reptiles that originates on the ilium and crosses the acetabulum and the knee joint before being inserted on the tibia.
The tendon of the ambiens muscle passes obliquely over the knee joint. It assists in the control of the bird’s toes. This muscle is present in some reptiles but not mammals. It is present in caiques and some other South American genera, but missing in most parrot genera. This was first noted by Garrod (1874) who proposed using this and other anatomical differences to classify parrots. For oproperty_value external_definitionanatomical differences among parrots see carotid arteries, furcula, and uropygial gland
One of two rows of feathers encircling the cloaca
FMA class may only represent the uterine portion
The second segment of the oviduct. This is where most of the egg white is added to the egg as it moves down the duct.
The third segment of the oviduct. At this point in the egg’s journey down the oviduct, the membranes form and calcification starts.
One of two lateral tracts connecting a uterus to a common median tract separated from the median vagina via ureters which prevent their fusion. Found in marsupials
A median canal in the reproductive system of marsupials that connects the uteri to a common tract, joining with the two lateral vaginas. Connects the uterine openings directly with the urogenital sinus
The anatomical space that is enclosed by a stomach.
Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585].
A anatomical cavity that is part of a ear vesicle.
A bump or swelling adorining the head and leading edge of a pectoral flipper, associated with the multiple joints and terminal phalanges as found in the multiple phalanges of the humpback whale
In a humpback the number of tubercles ranges from 9 to 11, with the first at the joint between the radius and metacarpal of digit II (with digit I absent)
Brodmann area 11 is one of Brodmann's cytologically defined regions of the brain. It is involved in planning, reasoning, and decision making.
A segmentation of the cerebral cortex on the basis of cytoarchitecture as described in Brodmann-1905, Brodmann-1909 and Brodmann-10. Maps for several species were presented. NeuroNames includes only areas in the human and in Old World monkeys. Of the latter, Brodmann studied representatives of several species including guenons (one Cercopithecus mona, one Cercocebus torquatus, and one Cercopithecus otherwise unspecified), which are all closely related African species, and one macaque (Macaca mulatta) an Asian species (Brodmann-1905). The legend to the summary map in Brodmann-1909 ascribes the areas simply to Cercopithecus. Brodmann referenced the areas by name and number. The same area number in humans and monkeys did not necessarily refer to topologically or cytoarchitecturally homologous structures. In NeuroNames the standard term for human areas consists of the English translation of Brodmann's Latin name followed by the number he assigned, e.g., agranular frontal area 6; the standard terms for monkey areas are in the format: area 6 of Brodmann-1909. He mapped a portion of areas limited to the banks of sulci, e.g., area 3 of Brodmann-1909 (Brodmann-1909) onto the adjacent, visible surface. This accounts for the fact that some areas appear larger on his surface map than on maps of other authors, e.g., area 3 of Vogts-1919. (Adapted from NeuroNames)
The retrosplenial region is a brain area and part of the cingulate cortex. It is defined by Brodmann area 26, Brodmann area 29 and the Brodmann area 30.
The term area 4 of Brodmann-1909 refers to a cytoarchitecturally defined portion of the frontal lobe of the guenon. It is located predominantly in the precentral gyrus. Brodmann-1909 regarded it as topographically and cytoarchitecturally homologous to the human gigantopyramidal area 4 and noted that it occupies a much greater fraction of the frontal lobe in the monkey than in the human. Distinctive features (Brodmann-1905): the cortex is unusually thick; the layers are not distinct; the cells are relatively sparsely distributed; giant pyramidal (Betz) cells are present in the internal pyramidal layer (V); lack of an internal granular layer (IV) such that the boundary between the external pyramidal layer (III) and the internal pyramidal layer (V) is indistinct; lack of a distinct external granular layer (II); a gradual transition from the multiform layer (VI) to the subcortical white matter.
Brodmann area 7 is one of Brodmann's cytologically defined regions of the brain. It is involved in locating objects in space. It serves as a point of convergence between vision and proprioception to determine where objects are in relation to parts of the body.
Brodmann area 8 is one of Brodmann's cytologically defined regions of the brain. It is involved in planning complex movements.
Brodmann area 12 is a subdivision of the cerebral cortex of the guenon defined on the basis of cytoarchitecture. It occupies the most rostral portion of the frontal lobe. Brodmann-1909 did not regard it as homologous, either topographically or cytoarchitecturally, to rostral area 12 of the human. Distinctive features (Brodmann-1905): a quite distinct internal granular layer (IV) separates slender pyramidal cells of the external pyramidal layer (III) and the internal pyramidal layer (V); the multiform layer (VI) is expanded, contains widely dispersed spindle cells and merges gradually with the underlying cortical white matter; all cells, including the pyramidal cells of the external and internal pyramidal layers are inordinately small; the internal pyramidal layer (V) also contains spindle cells in groups of two to five located close to its border with the internal granular layer (IV).
Brodmann area 13 is a subdivision of the cerebral cortex as defined on the guenon monkey and on the basis of cytoarchitecture. Brodmann area 13 is found in humans, however it seems to act as a bridge between the lateral and medial layers of the brain. Thus it is sometimes misidentified as not being a Brodmann area.
Brodmann Area 15 is one of Brodmann's subdivisions of the cerebral cortex in the brain. Area 15 was defined by Brodmann in the guenon monkey, but he found no equivalent structure in humans. However, functional imaging experiments have found structures that may be homologous.
Brodmann area 16 is a subdivision of the cerebral cortex of the guenon defined on the basis of cytoarchitecture. It is a relatively undifferentiated cortical area that Brodmann regarded as part of the insula because of the relation of its innermost multiform layer (VI) with the claustrum (VICl). The laminar organization of cortex is almost totally lacking. The molecular layer (I) is wide as in area 15 of Brodmann-1905. The space between layer I and layer VI is composed of a mixture of pyramidal cells and spindle cells with no significant number of granule cells. Pyramidal cells clump in the outer part to form glomeruli similar to those seen in some of the primary olfactory areas (Brodmann-1905). This term also refers to an area known as peripaleocortical claustral - a cytoarchitecturally defined (agranular) portion of the insula at its rostral extreme where it approaches most closely the claustrum and the prepyriform area (Stephan-76).
Brodmann area 21, or BA21, is part of the temporal cortex in the human brain. The region encompasses most of the lateral temporal cortex, a region believed to play a part in auditory processing and language. Language function is left lateralized in most individuals. BA21 is superior to BA20 and inferior to BA40 and BA41. This area is also known as middle temporal area 21. It is a subdivision of the cytoarchitecturally defined temporal region of cerebral cortex. In the human it corresponds approximately to the middle temporal gyrus. It is bounded rostrally by the temporopolar area 38 (H), ventrally by the inferior temporal area 20, caudally by the occipitotemporal area 37 (H), and dorsally by the superior temporal area 22 (Brodmann-1909). [WP,unvetted].
Brodmann area 22 is one of Brodmann's cytologically defined regions of the brain. It is involved in auditory processing.
The term area 23 of Brodmann-1909 refers to a subdivision of the cerebral cortex of the guenon defined on the basis of cytoarchitecture. Brodmann regarded it as topographically and cytoarchitecturally homologous to the combined ventral posterior cingulate area 23 and dorsal posterior cingulate area 31 of the human (Brodmann-1909). Distinctive Features (Brodmann-1905): the cortex is relatively thin; smaller cells predominate; the cell density of the multiform layer (VI) is great, producing a distinct boundary with the subcortical white matter; the internal granular layer (IV) is rather well developed; the internal pyramidal layer (V) contains a dense population of round, medium-sized ganglion cells concentrated at the border with layer IV; layers V and VI are narrow with a distinct mutual boundary.nn* Definition Source NeuroNames
Brodmann area 23, ventral posterior cingulate
Area 27 of Brodmann-1909 is a cytoarchitecturally defined cortical area that is a rostral part of the parahippocampal gyrus of the guenon (Brodmann-1909). It is commonly regarded as a synonym of presubiculum (Crosby-62). [WP,unvetted].
The Brodmann area 32, also known in the human brain as the dorsal anterior cingulate area 32, refers to a subdivision of the cytoarchitecturally defined cingulate region of cerebral cortex. In the human it forms an outer arc around the anterior cingulate gyrus. The cingulate sulcus defines approximately its inner boundary and the superior rostral sulcus (H) its ventral boundary; rostrally it extends almost to the margin of the frontal lobe. Cytoarchitecturally it is bounded internally by the ventral anterior cingulate area 24, externally by medial margins of the agranular frontal area 6, intermediate frontal area 8, granular frontal area 9, frontopolar area 10, and prefrontal area 11-1909. (Brodmann19-09). Dorsal region of anterior cingulate gyrus is associated with rational thought processes, most notably active during the Stroop task.
Brodmann area 32, dorsal anterior cingulate
Brodmann area 40, or BA40, is part of the parietal cortex in the human brain. The inferior part of BA40 is in the area of the supramarginal gyrus, which lies at the posterior end of the lateral fissure, in the inferior lateral part of the parietal lobe. It is bounded approximately by the intraparietal sulcus, the inferior postcentral sulcus, the posterior subcentral sulcus and the lateral sulcus. Cytoarchitecturally it is bounded caudally by the angular area 39 (H), rostrally and dorsally by the caudal postcentral area 2, and ventrally by the subcentral area 43 and the superior temporal area 22 (Brodmann-1909). Cytoarchitectonically defined subregions of rostral BA40/the supramarginal gyrus are PF, PFcm, PFm, PFop, and PFt. Area PF is the homologue to macaque area PF, part of the mirror neuron system, and active in humans during imitation. The supramarginal gyrus part of Brodmann area 40 is the region in the inferior parietal lobe that is involved in reading both in regards to meaning and phonology. [WP,unvetted].
A metapodium bone that is part of a digit 1 plus metapodial segment.
A metapodium bone that is part of a digit 2 plus metapodial segment.
A metapodial bone that is associated with digit III.
A metapodium bone that is part of a digit 4 plus metapodial segment.
A metapodium bone that is part of a digit 5 plus metapodial segment.
An element formed from the fusion of metapodium 3 and metapodium 4 (i.e. either metatarsals 3 and 4 or metacarpals 3 and 4).
this class can be used in annotation when it is unclear whether the element is a fusion of the metacarpal and metatarsal elements.
An element formed from the fusion of metacarpal 3 and metacarpal 4.
In many artiodactyls, the 3rd & 4th metapodials are fused, creating a main metapodial.
An element formed from the fusion of metatarsal 3 and metatarsal 4.
Regions of the cerebal cortex characterized by a particularly well-developed inner granular layer (layer 4); this type of cerebral cortex is represented by the primary sensory Brodmann area 17 of the visual cortex, Brodmann areas 1–3 of the somatic sensory cortex, and Brodmann area 41 of the auditory cortex.
A deep groove which runs transversely across the rostro-dorsal surface of the cerebrum and which is one of the landmarks on the cerebral cortex.
One of a set of small groups of neuron cell bodies located along the trajectory of optic fibers in the mesencephalon. These consist of the posterior nucleus [TA] (nucleus posterior [TA]), medial nucleus [TA] (nucleus medialis [TA]), and lateral nucleus [TA] (nucleus lateralis [TA]), which are also called the posterior, medial, and lateral terminal nuclei. The connections of these nuclei, along with the nucleus of the optic tract, make up the accessory optic system that appears to be concerned with retinal slip in specific directions
terminal nucleus of accessory optic tract
dorsal terminal nucleus of accessory optic tract
dorsal terminal nucleus of the accessory optic tract
posterior accessory nucleus of optic tract
posterior terminal nucleus of accessory optic tract
lateral terminal nucleus of the accessory optic tract
lateral accessory nucleus of optic tract
medial terminal nucleus of the accessory optic tract
The medial terminal nucleus is usually very prominent but it is reduced in primates (except, curiously, the tarsier), megachiropterans, Cynocephalus and Bradypus. Metatherians have a large medial terminal nucleus[Pettigrew et al. (1989)]
lateral geniculate nucleus magnocellular layer
magnocellular layer of lateral geniculate nucleus
Rods; necessary for the perception of movement, depth, and small differences in brightness[WP]
magnocellular layer of dorsal nucleus of lateral geniculate body
parvocellular layer of lateral geniculate nucleus
Cones; long- and medium-wavelength ("red" and "green" cones); necessary for the perception of color and form (fine details).[WP]
parvocellular layer of dorsal nucleus of lateral geniculate body
dorsal accessory nucleus of inferior olivary complex
medial accessory nucleus of inferior olivary complex
ventral accessory nucleus of inferior olivary complex
inferior olive ventral accessory nucleus
A ridge that girdles the base of a upper molar tooth
The fasciulus aberrans is a distinct bundle of fibers at the dorsal aspect of the anterior commisure. These fibers travel in the internal capsule between the putamen and caudate nuclei, and cross the midline to connect the dorsal neocortex of the two hemispheres. When the fasciculus aberrans is absent, the fibers connecting the neocortex of the two hemispheres takes a diffderent route through the external capsule[Johnson et al., (1982a, 1982b, 1994)]
konioocellular layer of lateral geniculate nucleus
koniocellular layer of dorsal nucleus of lateral geniculate body
A primary molar tooth that is part of a upper jaw region.
A secondary molar tooth that is part of a upper jaw region.
A primary molar tooth that is part of a lower jaw region.
A secondary molar tooth that is part of a lower jaw region.
Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand.
Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation.
Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.
A sesamoid element that is composed primarily of a cartilage tissue.
sesamoid cartilage of cricopharyngeal ligament
The intertrochanteric crest is a bony ridge located on the posterior side of the head of the femur, stretching obliquely downward and medially from the summit of the greater trochanter to the lesser trochanter. Together with the intertrochanteric line on the anterior side of the head, the crest mark the transition between of the neck of femur into the shaft of femur. An elevation between the middle and proximal third of the crest is known as the quadrate tubercle. The upper half of the crest forms the posterior border of the greater trochanter. The distal capsular attachment on the femur follows the shape of the irregular rim between the head and the neck. As a consequence, the capsule of the hip joint attaches in the region of the intertrochanteric line on the anterior side, but a finger away from the intertrochanteric crest on the posterior side of the head.
The intertrochanteric line (or spiral line of the femur) is a line located on the anterior side of the proximal end of the femur. The rough, variable ridge stretches between the lesser trochanter and the greater trochanter forming the base of the neck of the femur, roughly following the direction of the shaft of the femur. The iliofemoral ligament — the largest ligament of the human body — attaches above the line which also strengthen the capsule of the hip joint. The lower half, less prominent than the upper half, gives origin to the upper part of the Vastus medialis. Just like the intertrochanteric crest on the posterior side of the femural head, the intertrochanteric line mark the transition between the femural neck and shaft. The distal capsular attachment on the femur follows the shape of the irregular rim between the head and the neck. As a consequence, the capsule of the hip joint attaches in the region of the intertrochanteric line on the anterior side, but a finger away from the intertrochanteric crest on the posterior side of the head. The fibers of the ischiocapsular ligament attaches both on the joint capsule and to the intertrochanteric line.
The m. sphincter in the head region can be divided into 2 layers: M. sphincter colli profundus and superficialis; in studied placentals, the deepest layer has circular fibers, while the superficial layer has oblique and longitudinal fibers. In non-mammalian vertebrates (if differenciated) and in monotremes both the superficialis and the profundus layers are circular ('sphincter') muscles (Shumacher, 1956; Saban, 1971).
A epithelium that is part of a intestinal villus.
The prostate gland lobe that is located on the lateral side of the organ.
In carnivores, functions to hold on to meat as it is being cut by the teeth
A ring of ciliated tentacles surrounding the mouth
In the Entoprocta the anus is within the ring of the lophophore
The very first part of the duodenum which is slightly dilated.
A gland that is part of the gular region (throat)
The buccal nerve (also called the long buccal nerve) is a nerve in the face. It is a branch of the mandibular nerve (which is itself a branch of the trigeminal nerve) and transmits sensory information from skin over the buccal membrane (in general, the cheek) and from the second and third molar teeth.
External Pterygoid Nerve (or lateral pterygoid nerve): The nerve to the Pterygoideus externus frequently arises in conjunction with the buccinator nerve, but it may be given off separately from the anterior division of the mandibular nerve. It enters the deep surface of the muscle.
branch of buccal nerve to lateral pterygoid
The masseteric artery is small and passes laterally through the mandibular notch to the deep surface of the masseter muscle, which it supplies. It anastomoses with the masseteric branches of the external maxillary artery and with the transverse facial artery.
A tarsal bone that is formed from the fusion of the 1st and 2nd tarsal bones.
Subdivision of skeleton that is part of the velum and consists of a complex arrangement of thin cartilage rods and arches
Notochordal membrane covering derived from notochordal epithelium. Its first indication is at NF stage 24, and it is a distinct membrane by NF stage 28[XAO:0001020].
The notochordal sheath in amphioxus has a complex three-layered organization with the outer, middle and inner layer The outer and middle layer are composed of collagen fibers of different thickness and course, that correspond to collagen type I and collagen type III in vertebrates, respectively, and the inner layer is amorphous, resembles basal lamina, and is closely attached to the notochord by hemidesmosome junctions.
A diverticulum on the lingual aspect of the soft palate of male dromedaries which may be inflated with air and be extruded from the oral cavity during rut.
A fatty deposit found on the back of camels.
A bulbous ridge of highly vascularized tissue that runs along the center of the hard palate, expanding cranially to form two large lobes that terminate under the tip of the rostral palate, with another enlarged node at the caudal terminus.
A erectile tissue that is part of a corpus cavernosum maxillaris.
spongiose tissue of corpus cavernosum maxillaris
nerve ending of of corpus cavernosum maxillaris
A complex muscular and bony clasping and copulatory organ derived mainly from the pelvic fins, found under the head of male Phallostethoidea with the anus opening on one side and the genital pore on the other. The structure varies among family members. Hook-like ctenactia articulate basally with the aproctal axial which is movably articulated with the proctal axial bone itself, suspended anteriorly by the outer (and sometimes inner) pulvinular bone from the cleithrum and perhaps the urohyal. Other elements are the priapal ribs, the anteplural cartilage (supporting elements along with the cleithrum and the pulvinar), the toxactinium, the infrasulcar and the uncus (forming the claspers along with the ctenactinium), the penial, basipenial, papillary, prepapillary and cristate bones (forming the papillary unit).
Contains ducts from kidney, gonads, terminal parts of intestine[ISBN:047175644X]
A curved rod-like clasper on the posterior side of the priapium in Phallostethidae.
A long curved projection from the anterior end of the priapium in some Phallostethidae
he ventral element in the priapium of the Phallostethidae on which articulate the ctenactinia (q.v.). Also called aproctal or pelvic bone
An anatomical line of the face that connects the two inner (medial) canthi of the eye. The length of this line is known as the inter canthal distance.
A inner canthus that is part of a right eye.
A inner canthus that is part of a left eye.
Anatomical region comprising the peripheral part of the retina[XAO:0004458].
A dorsal thalamus that is in_the_left_side_of a diencephalon.
A dorsal thalamus that is in_the_right_side_of a diencephalon.
Anatomical space that is an opening in a bone of the skull.
Anatomical space which connects two or more compartment spaces or two or more anatomical cavities. Examples: foramen magnum, pyloric orifice, space of right inguinal canal, nutrient canal space,
A germinal center that is part of a tonsil.
consider adding related terms, e.g. secondary lymphoid tissue of tonsil
The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a tonsil[TS-1288].
Lymphoid tissue located in the appendix.
The buttocks are rounded portions of the anatomy located on the posterior of the pelvic region of apes and humans, including many other bipeds or quadrupeds.
Inframammary fold, inframammary crease or inframammary line is the feature of human anatomy which is a natural boundary of a breast from below, the place where the breast and the chest meet. The choice of the term depends on the prominence of the feature.
A neuropil that is part of a cerebral cortex [Automatically generated definition].
Vascular endothelium found in blood vessels of the blood-brain-barrier.
Vascular endothelium found in colon blood vessels.
The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule.
Epithelium lining the exocrine pancreas.
A hair in the frontal genital area of adolescent and adult humans, located on and around the sex organs, the crotch, and sometimes at the top of the inside of the thighs, in the pubic region around the pubis bone.
A strand of hair that is part of a axilla.
Musculature of the head and neck, spine, and ribs.
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
Anatomical projection that is part of the integumentl system.
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
The deep layer (fascia of Scarpa) is a layer of the anterior abdominal wall.
deep layer of superficial fascia of abdomen
membranous layer of subcutaneous tissue of abdomen
membranous layer of superficial fascia of abdomen
stratum membranosum telae subcutaneae abdominis
The anterior superior iliac spine (ASIS) is an important landmark of surface anatomy. It refers to the anterior extremity of the iliac crest of the pelvis, which provides attachment for the inguinal ligament, the sartorius muscle, and the tensor fasciae latae. ASIS provides a clue in identifying some other clinical landmarks, including: McBurney's point Gardner's line Roser-NC)laton line A - Anterior (front, like the face) S - Superior (towards the head, opposite to feet) I - Iliac S - Spine
The anterior inferior iliac spine (AIIS) is a bony eminence on the anterior border of the hip bone, or, more precisely, the wing of the ilium (i.e. the upper lateral parts of the pelvis).
The posterior border of the ala, shorter than the anterior, also presents two projections separated by a notch, the posterior superior iliac spine and the posterior inferior iliac spine. The posterior superior iliac spine serves for the attachment of the oblique portion of the posterior sacroiliac ligaments and the Multifidus.
The posterior border of the ala, shorter than the anterior, also presents two projections separated by a notch, the posterior superior iliac spine and the posterior inferior iliac spine. The posterior inferior iliac spine corresponds with the posterior extremity of the auricular surface.
A muscle that originates on the anterior iliac spine that passes through the inguinal canal before dividing into four branches, each attaching to a pouch nipple
In pouched marsupials, the ilio-marsupialis is less well developed, but may help in gland contraction to express milk during suckling (Griffiths & Slater, 1988) and it carries the genitofemoral nerve that innervates the mammary gland (Renfree, 1979) [doi:10.1046/j.1469-7580.2002.00087.x]
Associated with lumbar musculature. originally postulated to be involved in milk ejection, or for mammary support and for retraction of the teats.
in pouchless marsupials provides mechanical support for the attached young [doi:10.1046/j.1469-7580.2002.00087.x]
One of the branches of the ilio-marsupialis that attaches to a pouch nipple
The superficial inguinal ring is an anatomical structure in the anterior wall of the human abdomen. It is a triangular opening that forms the exit of the inguinal canal, which houses the ilioinguinal nerve, the genital branch of the genitofemoral nerve, and the spermatic cord (in men) or the round ligament (in women). At the other end of the canal, the deep inguinal ring forms the entrance. It is also called the subcutaneous inguinal ring or external inguinal ring. It is found within the aponeurosis of the external oblique, immediately above the crest of the pubis, 1 centimeter above and lateral to the pubic tubercle. It has medial and lateral crura. It is at the layer of the aponeurosis of the obliquus externus abdominis[Wikipedia:Superficial_inguinal_ring].
The dartos fascia is a fat-free layer of smooth muscular fiber outside the external spermatic fascia but below the skin. It is a continuation of Scarpa's Fascia which is a membranous layer of the subcutaneous tissue in the abdominal wall.
A dartos muscle that is part of a male reproductive system.
The tunica dartos acts to regulate the temperature of the testicles, which promotes spermatogenesis. It does this by expanding or contracting to wrinkle the scrotal skin. The wrinkled (rugose) appearance of the scrotum is due to this layer of fascia
the FMA class appears to belong here due to its synonyms.
A dartos muscle that is part of a female reproductive system.
The anterior talofibular ligament is a ligament in the ankle. It passes from the anterior margin of the fibular malleolus, anteriorly and medially, to the talus bone, in front of its lateral articular facet. It is one of the lateral ligaments of the ankle and prevents the foot from sliding forward in relation to the shin.
The posterior talofibular ligament, runs almost horizontally from the depression at the medial and back part of the fibular malleolus (lateral malleolus) to a prominent tubercle on the posterior surface of the talus immediately lateral to the groove for the tendon of the flexor hallucis longus.
Fluid contained within the notochordal canal
A specialized organ that is linked to the gut in beetles and host to a symbiotic yeast. The yeast cells assist in the digestion of less nutritious foods, supply needed B-vitamins and sterols, and provide resistance to certain toxins.
either of a pair of organs in an insect (as a true bug) that consist of a cellular mass of mycetocytes and are located one in either fat body. a cell in various insects (as most true bugs) of a type that contains unicellular and prob. symbiotic fungi and is usu. clustered with others of its kind into paired mycetomes. .
The auditory sensory organ of lizards, amphibians, and birds, which is homologous to the Corti in mammals.
consider classifying as a sensory epithelium
A sensory structure in the lagenar portion of an amphibian's membranous labyrinth between the oval and round windows.[AAO]
sensory epithelium of recessus basilaris
A tube leading from the external naris to the nasal cavity.
Nucleus of the medial ventral tegmental area, originally identified in the rat but also in cat, monkey and human, comprising an average of 7% volume of the VTA across the different species, with the largest being present in the cat.
Brain Info does not list the linear nuclei as part of the ventral tegmental area but as a co-area of the midbrain tegmentum. Am assuming the rostral linear nucleus of the raphe is synonymous, but needs further review. (NIF)
Nucleus identified in the medial ventral tegmental area that borders the red nucleus and superior cerebellar peduncle dorsally, the medial lemniscus laterally, the subtantia nigra pars compacta and paranigral nucleus ventrally and the rostral linear nucleus and interfascicular nucleus medially. Generally, the largest nucleus in the ventral tegmental area, occupying an average of 50% of the total volume as measured in rat, cat, monkey and human.
The basal portion (further from lumen) of an intestinal crypt. Contains multipotent stem cells. Stem cells in the crypts divide to form daughter cells. One daughter cell from each stem cell division is retained as a stem cell. The other becomes committed to differentiate along one of four pathways to become an enterocyte, enteroendocrine cell, goblet cell or Paneth cell.
Clearly defined prolifieration zones found in mammals. Not observed in agnathostomes, larval amphibians. Described in advanced species of fish and adult amphibians.
base part of epithelium of intestinal gland
The lateral parts of an intestinal crypt, continuous distally with the base and proximally with the intestinal villus epithelium.
wall part of epithelium of intestinal gland
A base of crypt of lieberkuhn that is part of a large intestine.
base of crypt of Lieberkuhn of large intestine
A wall of crypt of lieberkuhn that is part of a large intestine.
wall of crypt of Lieberkuhn of large intestine
The basal portion (further from lumen) of a intestinal crypt that is located in the small intestine.
base of crypt of Lieberkuhn of small intestine
The lateral parts of an intestinal crypt that is located in the small intestine, continuous distally with the base and proximally with the intestinal villus epithelium.
wall of crypt of Lieberkuhn of small intestine
A zone of the adrenal cortex located between the zona glomerulosa and the zona fasciculata.
currently postulated to be a site of initiation of adrenocyte proliferation and differentiation and a zone containing the adrenal cortical stem cells. Present in some rat species.
Endochondral element that is ventral, median, and associated with a single pharyngeal arch in the pharyngeal arch 3-7 skeleton.
Median ventral cartilage or bony element at the ventral point of a branchial arch, behind the tongue[http://www.fishbase.org/Glossary/Glossary.php?q=basibranchial&sc=is].
A basibranchial element that is cartilage. Basibranchial elements are ventral, median, and associated with a single pharyngeal arch in the pharyngeal arch 3-7 skeleton
A metaphysis that is part of a metaphysis.
A metaphysis that is part of a radius bone.
A diaphysis that is part of a metacarpal bone.
A distal epiphysis that is part of a metacarpal bone.
A organ component layer that is part of a integumental system.
One of two openings in the uterine cervix.
Opening of uterine cervix into the body of the uterus.
The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus].
Opening of uterine cervix into the vagina.
The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus].
The cavity formed by the walls of the cervix.
A reticular lamina of epithelium that is part of a sensory epithelium.
A nonampullary end of the superior or posterior semicircular ducts.
common membranous limb of membranous semicircular ducts
common membranous limb of semicircular ducts
crus membranaceum commune ductus semicircularis
crus membranaceum commune ductuum semicircularium
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
A fold of skin of the upper eyelid that partially covers the inner corner of the eye.
A plate of bone from the maxilla that that projects upward, medialward, and backward, by the side of the nose, forming part of its lateral boundary[WP,modified].
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
A organ cavity that is part of a uterus.
A nipple that is in_the_left_side_of a body proper.
A nipple that is in_the_right_side_of a body proper.
A diaphysis that is part of a metatarsal bone.
A zone of skin that is part of a palmar/plantar part of autopod.
A zone of skin that is part of a palmar part of manus.
A zone of skin that is part of a skin of pes.
The term nigrostriatal fibers refers to a dopaminergic fiber pathway connecting the substantia nigra with the striatum. It is not readily distinguished in myelin-stained cross-sections (Carpenter-83).
todo - connect this to dopamine related terms
Most superficial of 3 cytoarchitecturally defined layers of the piriform cortex, characterized by few neuronal cell bodies. It has been divided into a superficial part and a deep part.
Middle of three cytoarchitecturally defined layers of the piriform cortex characterized by a compact layer of cell bodies. It can be divided into a superficial part and a more densely packed deep part
Deepest of 3 cytoarchitecturally defined layers of the piriform cortex characterized by a moderately high density of pyramidal cells and large numbers of basal dendrites descending from pyramidal cells in layer 2.
An elongated nucleus consisting largely of multipolar spiny cells lying deep to the piriform cortex. According to Price (1990; pp. 979-998 in The Human Nervous System, G. Paxinos, (Ed.), Academic Press, San Diego), it is part of the claustrum.
Regional part of the inferior olivary complex
A group of cortical areas related by direct or indirect connectivity to the striate area 17 and functionally involved primarily in vision. They include the parastriate area 18, the peristriate area 19 and adjacent areas in the parietal lobe and temporal lobe (Adapted from BrainInfo and Zilles-1990).
Embryonic structure that gives rise to the telencephalon.
paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP]
A layer of fibrous and elastic fibers, taking the place of the submucosa in the larynx. It is divided by the laryngeal ventricle into two parts: the quadrangular membrane superiorly and the conus elasticus inferiorly.
Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells.
in future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology
Embryoid bodies are structures resembling embryos, occurring in several types of germ cell tumors[BTO].
The muscles of hand can be remembered using the mnemonic, 'A OF A OF A' for, Abductor pollicis brevis, Opponens pollicis, Flexor pollicis brevis, Adductor pollicis (thenar muscles) and Opponens digiti minimi, Flexor digiti minimi, Abductor digiti minimi (hypothenar muscles)[Wikipedia:Thenar_eminence].
Hypothenar refers to a group of three muscles of the palm that control the motion of the little finger. The three muscles are: Abductor digiti minimi Flexor digiti minimi Opponens digiti minimi
The Adductor hallucis (Adductor obliquus hallucis) arises by two headsboblique and transverse and is responsible for adducting the big toe. It is innervated by the lateral plantar nerve. It evolved from the contrahens I muscle as Man's ancestors' thumbs and big toes became opposable.
The flexor digitorum brevis lies in the middle of the sole of the foot, immediately above the central part of the plantar aponeurosis, with which it is firmly united. Its deep surface is separated from the lateral plantar vessels and nerves by a thin layer of fascia.
A patch of hair growing in the opposite direction of the rest of the hair.
Hair whorls occur in most hairy animals, on the body as well as on the head. Hair whorls, also known as crowns, swirls, trichoglyphs, or cowlicks, can be either clockwise or counterclockwise in direction of growth.[WP]
A collection of hairs that is part of a craniocervical region.
The entrance of the larynx is a triangular opening, narrow in front, wide behind, and sloping obliquely downward and backward. It is bounded, in front, by the epiglottis; behind, by the apices of the arytenoid cartilages, the corniculate cartilages, and the interarytenoid notch; and on either side, by a fold of mucous membrane, enclosing ligamentous and muscular fibers, stretched between the side of the epiglottis and the apex of the arytenoid cartilage; this is the aryepiglottic fold, on the posterior part of the margin of which the cuneiform cartilage forms a more or less distinct whitish prominence, the cuneiform tubercle. These folds form the upper borders of the quadrangular membrane.
Either of the the top and bottom portions of the vertebral bodies that interface with the vertebral discs. It is composed of a layer of thickened cancellous bone.
Mesenchyme that develops_from the neural crest[Automatically generated definition].
The simple cuboidal epithelium lining the lumen of kidney collecting ducts.
In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis
collecting duct of renal tubule epithelium
epithelium of collecting duct of renal tubule
A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae.
A muscular coat that is part of a ileum.
A sweat gland that is part of the skin of the palmar part of the manus or plantar part of the pes
in mice these are the only sweat glands present
sweat gland of palmar/plant part of autopod
Sweat that is produced by the glands on the palmar and plantar surfaces.
serves a purpose of increasing friction on the palms of hands or the pads of paws[WP]
Sweat that is produced by the glands of the axilla.
Encapsulated adipose tissue associated with the uterus
A proximal mesopodial endochondral element that is composed primarily of a bone tissue.
Encapsulated adipose tissue located between the scapulae.
A short projection from the base of the manubrium of the malleus, attached firmly to the drum membrane.
Muscle that is part of the respiratory system.
this class may be merged with 'respiratory system muscle'; check intercostals
A anatomical space that is enclosed by a sinusoid.
A sinusoidal space that is part of a hepatic sinusoid.
Any member of the network of tubes that return blood from the renal tissues to the systemic circulation.
we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta
A part of the body present only in a specific gender.
A part of the body present only in males.
A part of the body present only in females.
A larval stage of that is the immature stage of some invertebrates that undergoe gradual metamorphosis (hemimetabolism) before reaching its adult stage.
Any of various immature insects; especially: a larva of an insect (as a grasshopper, true bug, or mayfly) with incomplete metamorphosis that differs from the imago especially in size and in its incompletely developed wings and genitalia[BTO:0000954].
The free-swimming first stage of the larva of certain crustaceans, having an unsegmented body with three pairs of appendages and a single median eye. The eye is known for that reason as the 'naupliar eye', and is often absent in later developmental stages, although it is retained into the adult form in some groups, such as the Notostraca.
A crustacean larva in usually the first stage after leaving the egg and with three pairs of appendages, a median eye, and little or no segmentation[BTO:0000915].
A process projecting backward and downward from the acromion of the scapula of some mammals.
On the dorsal border of the wing of the ilium , at it's junction with the shaft is a cut away. This forms the Greater sciatic notch. The sciatic nerve runs over the notch in passage to the hindlimb.
deep indentation in the posterior border of the hip bone at the point of union of the ilium and ischium[HP:0010456].
Either of two notches on the dorsal border of the hip bone on each side that when closed off by ligaments form the corresponding sciatic foramina.
Below the ischial spine is a smaller notch, the lesser sciatic notch; it is smooth, coated in the recent state with cartilage, the surface of which presents two or three ridges corresponding to the subdivisions of the tendon of the Obturator internus, which winds over it. It is converted into a foramen, the lesser sciatic foramen, by the sacrotuberous and sacrospinous ligaments, and transmits the tendon of the Obturator internus, the nerve which supplies that muscle, and the internal pudendal vessels and nerve.
Is part of the pelvis on the edge of the wing of the ilium. Round in shape, dorsal to the pubis and ischium. Acts as structrure that muscles can attach too.
The superior pubic ramus is a part of the pubic bone which forms a portion of the obturator foramen. It extends from the body to the median plane where it articulates with its fellow of the opposite side. It is conveniently described in two portions, viz. , a medial flattened part and a narrow lateral prismoid portion.
The inferior pubic ramus is thin and flattened. It passes lateralward and downward from the medial end of the superior ramus; it becomes narrower as it descends and joins with the inferior ramus of the ischium below the obturator foramen.
The ischiopubic ramus is a compound structure consisting of the following two structures: from the pubis, the inferior pubic ramus from the ischium, the inferior ramus of the ischium It serves as part of the origin for the Obturator internus muscle. It also marks a vertex of the anal triangle and the urogenital triangle. The fascia of Colles is attached to its margin.
The superior ramus of the ischium (descending ramus) projects downward and backward from the body and presents for examination three surfaces: external, internal, and posterior. The external surface is quadrilateral in shape. It is bounded above by a groove which lodges the tendon of the Obturator externus; below, it is continuous with the inferior ramus; in front it is limited by the posterior margin of the obturator foramen; behind, a prominent margin separates it from the posterior surface. In front of this margin the surface gives origin to the Quadratus femoris, and anterior to this to some of the fibers of origin of the Obturator externus; the lower part of the surface gives origin to part of the Adductor magnus. The internal surface forms part of the bony wall of the lesser pelvis. In front it is limited by the posterior margin of the obturator foramen. Below, it is bounded by a sharp ridge which gives attachment to a falciform prolongation of the sacrotuberous ligament, and, more anteriorly, gives origin to the Transversus perinC&i and Ischiocavernosus. Posteriorly the ramus forms a large swelling, the tuberosity of the ischium
The Inferior Ramus of the ischium (ascending ramus) is the thin, flattened part of the ischium, which ascends from the superior ramus, and joins the inferior ramus of the pubisbthe junction being indicated in the adult by a raised line. The outer surface is uneven for the origin of the obturator externus and some of the fibers of the adductor magnus; its inner surface forms part of the anterior wall of the pelvis. Its medial border is thick, rough, slightly everted, forms part of the outlet of the pelvis, and presents two ridges and an intervening space. The ridges are continuous with similar ones on the inferior ramus of the pubis: to the outer is attached the deep layer of the superficial perineal fascia (fascia of Colles), and to the inner the inferior fascia of the urogenital diaphragm. If these two ridges be traced downward, they will be found to join with each other just behind the point of origin of the transversus perinC&i; here the two layers of fascia are continuous behind the posterior border of the muscle. To the intervening space, just in front of the point of junction of the ridges, the transversus perinC&i is attached, and in front of this a portion of the crus penis vel clitoridis and the ischiocavernosus. Its lateral border is thin and sharp, and forms part of the medial margin of the obturator foramen.
The acetabular fossa is the roughened depression in the centre of the acetabulum, surrounded by the lunate acetabular surface and the acetabular notch. The acetabular fossa provides an insertion point for the teres ligaments that secure the femoral head.
It is occupied by the ligament of head of femur[WP]
The acetabulum presents below a deep notch, the acetabular notch, which is continuous with a circular non-articular depression, the acetabular fossa, at the bottom of the cavity: this depression is perforated by numerous apertures, and lodges a mass of fat. The notch is converted into a foramen by the transverse ligament; through the foramen nutrient vessels and nerves enter the joint; the margins of the notch serve for the attachment of the ligament of the head of the femur.
A collection of feathers arranged in a concave pattern surrounding the eyes in some birds, particularly owls.
A collection of feathers found on the heads of some owls.
Any of the groups of neurons located between the thalamus and midbrain that receive binocular sensory input from retinal ganglion cells of the eyes and are responsible for maintaining the pupillary light reflex
A taste bud that is located on the tongue, situated on a gustatory papilla.
A gustatory epithelium that is part of a tongue.
A gustatory epithelium that is part of a roof of mouth.
Subcutaneous adipose tissue that is located in the peritoneal cavity.
Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041].
Subcutaneous adipose tissue that is located in the abdominal region.
The extraperitoneal space is the portion of the abdomen and pelvis which does not lie within peritoneum. It includes: Retroperitoneal space Retropubic space The space in the pelvis is divided into the following components: prevesical space perivesical space perirectal space
obsolete as it groups developmentally very different structures
A bulbospongiosus muscle that is part of a female reproductive system.
One of two bilaterally symmetrical holes (fenestrae) in the temporal bone.
A temporal fenestra in the upper part of the temporal bone.
An infratemporal fenestra, also called the lateral temporal fenestra is an opening in the skull behind the orbit in some animals.
A cnida that is glutinous and is capable of sticking to prey. Found on burrowing (tube) anemones, which help create the tube in which the animal lives.
Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery.
Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion].
Encapsulated adipose tissue associated with the kidney
An antorbital fenestra is an opening in the skull, in front of the eye sockets. This skull formation first appeared in archosaurs during the Triassic Period. Living birds today possess antorbital fenestrae, but the feature has been lost in modern crocodilians. In some archosaur species, the opening has closed but its location is still marked by a depression, or fossa, on the surface of the skull. This is called an antorbital fossa.
Fissure between cerebellar hemispheric lobules VIIBi and VIIBii.
The monticulus of the cerebellum is divided by the primary fissure (or preclival fissure) into an anterior, raised part, the culmen or summit, and a posterior sloped part, the clivus; the quadrangular lobule is similarly divided.
Fissure between cerebellar lobules I and II.
A duct in ammocetes (larval lamprey) that is reputed to connect the endostylar lumen to the pharyngeal lumen. Resembles the thyroglossal duct.
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage.
An appendage formed by the fusion of the nose and upper lip.
An area of skin adjacent to the female external genitals of various lower primates that undergo marked alteration in turgidity and often in color during estrus.
An area of hardened, leathery skin on either side of the base of the tail on the rump.
A distal phalanx that is part of a digit 1 [Automatically generated definition].
A distal phalanx that is part of a digit 2 [Automatically generated definition].
A distal phalanx that is part of a digit 3. In odd-toes ungulates (Perissodactyla e.g. horses) this is called the coffin bone. In even-toed ungulates (Artiodactyla e.g cattle) this is associated with the medial claw.
the bottommost bone in the equine leg and is encased by the hoof capsule. The distal phalanx articulates with both the middle phalanx and the distal sesamoid, forming the distal interphalangeal joint[Wikipedia:Coffin_bone]
A distal phalanx that is part of a digit 4 [Automatically generated definition].
A distal phalanx that is part of a digit 5 [Automatically generated definition].
A middle phalanx that is part of a digit 2 [Automatically generated definition].
A middle phalanx that is part of a digit 3 [Automatically generated definition].
A middle phalanx that is part of a digit 4 [Automatically generated definition].
A middle phalanx that is part of a digit 5 [Automatically generated definition].
A proximal phalanx that is part of a autopod digit 1 [Automatically generated definition].
proximal phalanx of first digit of autopod
A proximal phalanx that is part of a autopod digit 2 [Automatically generated definition].
proximal phalanx of 2nd digit of autopod
proximal phalanx of second digit of autopod
A proximal phalanx that is part of a autopod digit 3 [Automatically generated definition].
proximal phalanx of 3rd digit of autopod
proximal phalanx of third digit of autopod
A proximal phalanx that is part of a autopod digit 4 [Automatically generated definition].
proximal phalanx of 4th digit of autopod
proximal phalanx of fourth digit of autopod
A proximal phalanx that is part of a autopod digit 5 [Automatically generated definition].
proximal phalanx of 5th digit of autopod
proximal phalanx of fifth digit of autopod
A distal inter-phalangeal joint that is part of the 3rd digit.
In Equidae, this is known as the coffin joint, and is the articulation between the short pastern bone (P2) and the coffin bone (P3 / distal phalanx)
distal interphalangeal joint of digit III
equine second interphalangeal joint of limb digit III
A distal inter-phalangeal joint that is part of the 3rd pedal digit.
distal interphalangeal joint of pedal digit III
distal interphalangeal joint of third digit of foot
distal interphalangeal joint of third toe
equine distal interphalangeal joint of hindlimb
distal interphalangeal joint of pedal digit 3
A distal inter-phalangeal joint that is part of the 3rd manual digit.
distal interphalangeal joint of manual digit III
distal interphalangeal joint of middle finger
equine distal interphalangeal joint of forelimb
equine second interphalangeal joint of forelimb digit III
distal interphalangeal joint of manual digit 3
A short wide fibrous structure that attaches proximally to the navicular (distal sesamoid) and distally to the palmar margin of the flexor surface of the distal phalanx
A muscular sheet of the omasum consisting of two lateral layers and an intermediate layer of smooth muscle covered with non-glandular stratified squamous epithelium
anterodorsal nucleus of medial geniculate complex
anterodorsal nucleus of the medial geniculate body
nucleus corporis geniculati medialis, pars anterodorsalis
anterodorsal nucleus of medial geniculate body
dorsolateral nucleus of oculomotor nuclear complex
A division of oculomotor nuclear complex that exists in organisms with electric organs which is responsible for eye movements.
oculomotor division of oculomotor nuclear complex
A division of oculomotor nuclear complex that exists in organisms with electric organs which has axons terminating in the electric organs.
electromotor division of oculomotor nuclear complex
limb of internal capsule of telencephalon
Portion of internal capsule lying between the lenticular nucleus and the head of the caudate nucleus.
The anterior limb of internal capsule (or frontal part) contains: (1) fibers running from the thalamus to the frontal lobe; (2) fibers connecting the lentiform and caudate nuclei; (3) fibers connecting the cortex with the corpus striatum; and (4) fibers passing from the frontal lobe through the medial fifth of the base of the cerebral peduncle to the nuclei pontis[Wikipedia:Anterior_limb_of_internal_capsule].
the streaming fibers of the anterior internal capsule separate the caudate nucleus and putamen in the human brain (in the mouse brain the caudoputamen is continuous)[ISBN10:0123813611]
Portion of internal capsule lying between the globus pallidus and the thalamus (Nolte, The Human Brain, 6th ed., 2009, pg 409, modified by MM)
Thin band of fibers separating the claustrum from the insular cortex
Extreme capsule is an organ subdivision of the telencephalon which is made up primarily of myelinated axonal neural tissue (white matter). The extreme capsule is a sheet-like fiber bundle located lateral to the clausturm and medial to the insula which projects dorsally to the white matter underlying the cerebral cortex[FMA:61960].
The extreme capsule is a long association fiber pathway of white matter in the brain that provides bidirectional communication between such areas as the claustrum and the insular cortex, and the inferior frontal gyrus and the middle-posterior portion of the superior temporal gyrus. Its fibers are near to but can be distinguished by MRI tractography from adjacent fiber bundles such as the uncinate fasciculus, the external capsule, the arcuate fascicle, and the medial, inferior and superior longitudinal fascicles. Given its bidirectional connection between the Broca's and Werniche's speech areas it could have a role in language[Wikipedia:Extreme_capsule, http://en.wikipedia.org/wiki/Extreme_capsule].
The lenticular fasciculus is a tract connecting the globus pallidus to the Thalamic fasciculus. The thalamic fasciculus (composed of the lenticular fasciculus and ansa lenticularis) runs into the Thalamus. It connects the globus pallidus to the thalamus.
FMA appears to divide this into diencephalon and telencephalon parts
white matter lamina of cerebral hemisphere
Medullary laminae of thalamus are layers of myelinated fibres that appear on cross sections of the thalamus. They also are commonly referred to as laminae medullares thalami or medullary layers of thalamus. The specific layers are: Lamina medullaris lateralis (external medullary lamina) - separates ventral and lateral thalamus from the subthalamus and thalamic reticular nucleus; Lamina medullaris medialis (internal medullary lamina) - positioned between the dorsomedial and ventral nuclei of thalamus, encloses the intralaminar nuclei (centromedian nucleus, paracentral, and central lateral)
A medullary lamina that separates ventral and lateral thalamus from the subthalamus and thalamic reticular nucleus.
external medullary lamina of the thalamus
A subdivision of the central canal of the spinal cord along its anterior-posterior axis. This is typically subdivided into cervical, thoracic, lumbar and sacral segments
regional part of spinal cord central canal
subdivision of spinal cord central canal
Part of fornix extending from the body that curves ventrally rostral to the crossing of the anterior commissure ending in the septal nuclei
The white laminae of cerebellum is subdivision of the cerebellar cortex comprised of myelinated axons lying deep to the granule cell layer of the cerebellar cortex.
Part of spinal cord central canal contained in the thoracic spinal cord. It is continuous rostrally with the cervical spinal cord central canal and caudally with the lumbar spinal cord central canal.
Part of central canal contained within the cervical spinal cord. It is continuous caudally with the thoracic spinal cord central canal and rostrally with the fourth ventricle of the brain via the obex
Part of central canal lying within the lumbar spinal cord. It is continuous rostrally with the central canal of the thoracic spinal cord and caudally with the central canal of the sacral spinal cord.
The term frontomarginal sulcus (H) refers to a superficial feature of the human frontal lobe; it is located at the rostral margin of the orbital surface of the lobe (Ono-90). (NN)
Part of spinal cord central canal contained in the sacral spinal cord. It is continuous rostrally with the spinal cord central canal of the lumbar cord.
CA1 part of stratum pyramidale hippocampi
Part of pyramidal cell layer in area CA2, lying superficial to the CA2 stratum oriens, and deep to the stratum radiatum of CA2, continuous with the pyramidal cell layers of CA1 and CA3
CA2 part of stratum pyramidale hippocampi
A layer of hippocampal field that is part of a hippocampus pyramidal layer and is part of a CA3 field of hippocampus.
CA3 part of stratum pyramidale hippocampi
Part of stratum oriens lying in area CA3 deep to the CA3 pyramidal cell layer and continuous with stratum oriens of area CA2 and bounded by the dentate gyrus hilus.
Part of stratum oriens lying in area CA1, superficial to the alveus of CA1 and deep to the pyramidal cell layer of CA1. It is continuous with the stratum oriens of CA2 and bounded by the subiculum
Part of stratum radiatum lying in area CA1, superficial to the CA1 pyramidal cell layer and deep to the CA1 stratum lucidum-moleculare, continuous with the stratum radiatum of CA2 and bounded by the subiculum. It contains the Schaffer collateral projection from CA3.
Part of stratum radiatum in area CA2, lying superficial to the pyramidal cell layer and deep to CA2 stratum lacunosum-moleculare, continuous with the stratum radiatum of CA1 and CA3.
Part of stratum radiatum in area CA3, lying superficial to the stratum lucidum and deep to CA3 stratum lacunosum-moleculare.
Part of stratum lacunosum-moleculare lying in area CA1, superficial to CA1 stratum radiatum and bounded by the pial surface, continuous with stratum lacunosum-moleculare of CA2 and the subiculum stratum moleculare
CA1 part of stratum lacunosum moleculare
stratum lacunosum moleculare of the CA1 field
Part of stratum lacunosum-moleculare lying in area CA2, superficial to the CA2 stratum radiatum, that is continuous with the stratum lacunosum-moleculare in areas CA3 and CA1
CA2 part of stratum lacunosum moleculare
stratum lacunosum moleculare of the CA2 field
Part of stratum lacunosum-moleculare in area CA3. It is bounded by the stratum lacunosum-moleculare of CA2 and CA1. It is bounded superficially by the pial surface and deep by the CA3 stratum radiatum. It is continuous with the stratum lacunosum-moleculare of CA2.
CA3 part of stratum lacunosum moleculare
stratum lacunosum moleculare of the CA3 field
A layer of hippocampal field that is part of a CA3 field of hippocampus and is part of a hippocampus stratum lucidum.
A subdivision of a layer of the hippocampus (e.g. stratum moleculare) covering all or port of a hippocampal field (e.g. CA1).
Part of dorsal tegmental nucleus characterized by round, small cells that are lightly stained in Nissl preparations.
According to Hayakawa and Zuo (1983), the TDD cannot be clearly identified in the tree shrew or in human
dorsal tegmental nucleus of gudden pars dorsalis
Cytoarchitectural part of the dorsal tegmental nucleus based on cell size. The pars ventralis is characterized by medium sized oval or triangular cells that stain darkly in NIssl stains.
According to Hayakawa and Zuo (1983), the TDV cannot be clearly identified in the tree shrew or in human
dorsal tegmental nucleus of gudden pars ventralis
pars ventralis of the dorsal tegmental nucleus
pars ventralis of the dorsal tegmental nucleus of gudden
Part of alveus lying within hippocampal sector CA3
anterior nucleus of hypothalamus anterior part
anterior hypothalamic nucleus anterior part
anterior hypothalamic nucleus, anterior part
anterior nucleus of hypothalamus central part
anterior hypothalamic area, central part
anterior hypothalamic nucleus central part
anterior hypothalamic nucleus, central part
anterior nucleus of hypothalamus posterior part
anterior hypothalamic nucleus posterior part
anterior hypothalamic nucleus, posterior part
anterior nucleus of hypothalamus dorsal part
anterior hypothalamic nucleus dorsal part
anterior hypothalamic nucleus, dorsal part
paraventricular nucleus of the hypothalamus descending division - medial parvicellular part, ventral zone
paraventricular hypothalamic nucleus medial parvicellular part, ventral zone
paraventricular hypothalamic nucleus, descending division, medial parvicellular part, ventral zone
paraventricular nucleus of the hypothalamus, descending division, medial parvicellular part, ventral zone
paraventricular nucleus of the hypothalamus descending division - dorsal parvicellular part
paraventricular hypothalamic nucleus dorsal parvicellular part
paraventricular hypothalamic nucleus, descending division, dorsal parvicellular part
paraventricular nucleus of the hypothalamus, descending division, dorsal parvicellular part
paraventricular nucleus of the hypothalamus descending division - lateral parvicellular part
paraventricular hypothalamic nucleus lateral parvicellular part
paraventricular hypothalamic nucleus, descending division, lateral parvicellular part
paraventricular nucleus of the hypothalamus, descending division, lateral parvicellular part
paraventricular nucleus of the hypothalamus descending division - forniceal part
paraventricular hypothalamic nucleus forniceal part
paraventricular hypothalamic nucleus, descending division, forniceal part
paraventricular nucleus of the hypothalamus, descending division, forniceal part
paraventricular nucleus of the hypothalamus, parvicellular division forniceal part
paraventricular nucleus of the hypothalamus magnocellular division - anterior magnocellular part
paraventricular hypothalamic nucleus anterior magnocellular part
paraventricular hypothalamic nucleus, magnocellular division, anterior magnocellular part
paraventricular nucleus of the hypothalamus, magnocellular division, anterior magnocellular part
paraventricular nucleus of the hypothalamus magnocellular division - medial magnocellular part
paraventricular hypothalamic nucleus medial magnocellular part
paraventricular hypothalamic nucleus, magnocellular division, medial magnocellular part
paraventricular nucleus of the hypothalamus, magnocellular division, medial magnocellular part
paraventricular nucleus of the hypothalamus magnocellular division - posterior magnocellular part
paraventricular hypothalamic nucleus posterior magnocellular part
paraventricular hypothalamic nucleus, magnocellular division, posterior magnocellular part
paraventricular nucleus of the hypothalamus, magnocellular division, posterior magnocellular part
paraventricular nucleus of the hypothalamus descending division
paraventricular hypothalamic nucleus, descending division
paraventricular nucleus of the hypothalamus, descending division
paraventricular nucleus of the hypothalamus magnocellular division
paraventricular hypothalamic nucleus magnocellular division
paraventricular hypothalamic nucleus, magnocellular division
paraventricular nucleus of the hypothalamus, magnocellular division
paraventricular nucleus of the hypothalamus parvicellular division
paraventricular hypothalamic nucleus parvicellular division
paraventricular hypothalamic nucleus, parvicellular division
paraventricular nucleus of the hypothalamus, parvicellular division
The ventral portion of the dorsal striatum, linking the caudate nucleus and the putamen anteriorly (adapted from Wikipedia)
A spinal cord lateral horn that is part of a thoracic spinal cord.
A dorsal horn of spinal cord that is part of a thoracic spinal cord.
A ventral horn of spinal cord that is part of a thoracic spinal cord.
apex of thoracic spinal cord dorsal horn
apex of thoracic spinal cord posterior horn
Substantia gelatinosa of thoracic spinal cord posterior horn
substantia gelatinosa of thoracic spinal cord dorsal horn
A gray matter of spinal cord that is part of a cervical spinal cord.
A white matter of spinal cord that is part of a cervical spinal cord.
A nerve root that is part of a accessory XI nerve.
accessory portion of spinal accessory nerve
cranial portion of eleventh cranial nerve
dorsal nerve root of thoracic spinal cord
posterior nerve root of thoracic spinal cord
ventral nerve root of thoracic spinal cord
anterior nerve root of thoracic spinal cord
A spinal cord lateral horn that is part of a cervical spinal cord.
A dorsal horn of spinal cord that is part of a cervical spinal cord.
A ventral horn of spinal cord that is part of a cervical spinal cord.
apex of cervical spinal cord dorsal horn
apex of cervical spinal cord posterior horn
A substantia gelatinosa that is part of a cervical spinal cord dorsal horn.
substantia gelatinosa of cervical spinal cord dorsal horn
substantia gelatinosa of cervical spinal cord posterior horn
vestibular fissure of the cochlear canal
commissura grisea anterior medullae spinalis
commissura grisea posterior medullae spinalis
posterior grey commissure of spinal cord
apex of lumbar spinal cord posterior horn
A substantia gelatinosa that is part of a lumbar spinal cord dorsal horn.
substantia gelatinosa of lumbar spinal cord dorsal horn
substantia gelatinosa of lumbar spinal cord posterior horn
A ventral root of spinal cord that overlaps a cervical spinal cord.
ventral nerve root of cervical spinal cord
anterior nerve root of cervical spinal cord
A dorsal root of spinal cord that overlaps a cervical spinal cord.
dorsal nerve root of cervical spinal cord
posterior nerve root of cervical spinal cord
A gray matter of spinal cord that is part of a thoracic spinal cord.
A white matter of spinal cord that is part of a thoracic spinal cord.
A dorsal horn of spinal cord that is part of a lumbar spinal cord.
A sulcus of brain that is part of a frontal cortex.
A gyrus that is part of a occipital lobe.
A nerve root that extends_fibers_into a terminal nerve.
A phylogenetic subdivision of the cerenellum, the oldest part, which regulates balance and eye movements. It receives vestibular input from both the semicircular canals and from the vestibular nuclei, and sends fibres back to the medial and lateral vestibular nuclei. It also receives visual input from the superior colliculi and from the visual cortex (the latter via the pontine nuclei, forming a cortico-ponto-cerebellar pathway). Lesions of the vestibulocerebellum cause disturbances of balance and gait.
A phylogenetic subdivision of the cerenellum, the intermediate part, which regulates body and limb movements. It receives proprioception input from the dorsal columns of the spinal cord (including the spinocerebellar tract) and the trigeminal nerve, as well as from visual and auditory systems. It sends fibres to deep cerebellar nuclei which in turn project to both the cerebral cortex and the brain stem, thus providing modulation of descending motor systems.
A phylogenetic subdivision of the cerenellum, the newest part, which is involved in planning movement and evaluating sensory information for action. It receives input exclusively from the cerebral cortex (especially the parietal lobe) via the pontine nuclei (forming cortico-ponto-cerebellar pathways), and sends fibres mainly to the ventrolateral thalamus (in turn connected to motor areas of the premotor cortex and primary motor area of the cerebral cortex) and to the red nucleus (in turn connected to the inferior olivary nucleus, which links back to the cerebellar hemispheres).
the most lateral paired regions of the cerebellum; the lateral zone receives input from the parietal cortex via pontocerebellar mossy fibers regarding the location and position of the body and integrates input signals with indications of muscle activit[MP:0009965]y
A nucleus present in the ventral tegmentum of squalomorph sharks.
A nucleus present in the ventral tegmentum of skates.
A multi-tissue structure that is part of a anterior lobe of cerebellum and is part of a cerebellar hemisphere.
hemisphere of anterior lobe of cerebellum
hemisphere part of cerebellar anterior lobe
A multi-tissue structure that is part of a cerebellar hemisphere and is part of a posterior lobe of cerebellum.
hemisphere of posterior lobe of cerebellum
hemisphere part of cerebellar posterior lobe
A white matter that is part of a medulla oblongata.
A nerve cell nucleus situated in the dorsal portion of the intermediate hypothalamic region.
The fish catecholamines originate in two large aggregations of neurons: the nucleus recessus lateralis (NRL) and the nucleus recessus posterioris (NRP). The nuclei were found in the hypothalamus of numerous species, e.g., the gold fish, eel, and roach.
The nucleus preopticus (NPO) of the hypothalamus of common carp, is a homolog of the paraventricular nucleus of mammals.
A small nucleus at the base of the hypothalamus, adjacent to the arcuate nucleus.
periventricular nucleus of the hypothalamus
distal interphalangeal joint of index finger
distal interphalangeal joint of manual digit II
distal interphalangeal joint of manual digit 2
distal interphalangeal joint of manual digit IV
distal interphalangeal joint of ring finger
distal interphalangeal joint of manual digit 4
distal interphalangeal joint of little finger
distal interphalangeal joint of manural digit V
distal interphalangeal joint of manural digit 5
distal interphalangeal joint of pedal digit II
distal interphalangeal joint of second digit of foot
distal interphalangeal joint of second toe
distal interphalangeal joint of pedal digit 2
distal interphalangeal joint of fourth digit of foot
distal interphalangeal joint of fourth toe
distal interphalangeal joint of pedal digit IV
distal interphalangeal joint of pedal digit 4
distal interphalangeal joint of fifth digit of foot
distal interphalangeal joint of fifth toe
distal interphalangeal joint of little toe
distal interphalangeal joint of pedal digit V
distal interphalangeal joint of pedal digit 5
A distal interphalangeal joint that is part of a digit 2.
check whether NCITA classes belong with hand or generic autopod
distal interphalangeal joint of digit II
A distal interphalangeal joint that is part of a digit 4.
distal interphalangeal joint of digit IV
A distal interphalangeal joint that is part of a digit 5.
A tooth whorl located at or near the mandibular symphysis.
A tooth whorl found in extinct holocephalids, in which the teeth in the center of the spiral are smallest and oldest, probably occupying the entire mandibular arch.
The pterygoid plexus is a venous plexus of considerable size, and is situated between the temporalis muscle and lateral pterygoid muscle, and partly between the two pterygoid muscles.
The angular vein formed by the junction of the frontal vein and supraorbital vein, runs obliquely downward, on the side of the root of the nose, to the level of the lower margin of the orbit, where it becomes the anterior facial vein. It receives the external nasal veins of the ala nasi, and communicates with the superior ophthalmic vein through the nasofrontal vein, thus establishing an important anastomosis between the anterior facial vein and the cavernous sinus.
Any of three grooves in the temporal lobe including the inferior, middle, and superior temporal sulci.
A groove or cleft that divides the outer surface of the temporal lobe running in the same direction but at a lower level to the superior temporal sulcus.
The Left gastric vein (or coronary vein) carries blood low in Oxygen, tributaries derived from both surfaces of the stomach; it runs from right to left along the lesser curvature of the stomach, between the two layers of the lesser omentum, to the esophageal opening of the stomach, where it receives some esophageal veins. It then turns backward and passes from left to right behind the omental bursa and drains into the portal vein. Esophageal and paraesophageal varices are primarily supplied by the left gastric vein and typically drain into the azygos/hemiazygos venous system.
The right gastric vein, also known as the pyloric vein, drains blood from the lesser curvature of the stomach into the hepatic portal vein. It is part of the portal circulation.
The superficial epigastric vein is a vein which travels with the superficial epigastric artery. It joins the accessory saphenous vein near the fossa ovalis.
The posterior auricular artery is a small artery and arises from the external carotid artery, above the Digastric muscle and Stylohyoid muscle, opposite the apex of the styloid process. It ascends posteriorly beneath the parotid gland, along the styloid process of the temporal bone, between the cartilage of the ear and the mastoid process of the temporal bone along the lateral side of the head. The posterior auricular artery supplies blood to the scalp posterior to the auricle and to the auricle itself.
The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint.
The anterior choroidal artery originates from the internal carotid artery, though it also rarely arises from the middle cerebral artery.
A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component.
A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component.
A epithelium that is part of a frontonasal prominence.
A unilaminar epithelium that develops_from a ectoderm and is part of a anal region.
A anatomical space that is enclosed by a pleuroperitoneal canal.
A epithelium that is part of a median lingual swelling.
A paired plastron element that is in the anterior part of the plastron, anterior to the hypoplastron, posterior to the epiplastron and adjacent to the median entoplastron.
One of a series of plates on each side of the carapace, forming two rows between the peripheral plates and the median neural plates.
A primordium that gives rise to a carapace.
A longitidunial ridge on the lateral aspect of the flank that appears in the late pharyngula stage of chelonians. It forms the leading edge of the laterally expanding carapacial primordium.
A mesenchyme that is part of a carapacial ridge.
A epithelium that is part of a carapacial ridge.
A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells.
A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular
A duct that is located etween lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory.
A small duct which drains individual secretory units. These are usually inconspicuous, lined by a simple epithelium consisting of low cuboidal cells.
A intercalated duct that is part of a pancreas.
The tiny tubules with a very thin epithelial layer in the salivary glands running from the salivary acini into the striated duct.
Consider adding a generic 'striated duct' class
A circular structural unit of bone tissue. It consists of a central hole, the Haversian canal through which blood vessels run, surrounded by concentric rings, called lamellae.
Haversian canals are a series of tubes around narrow channels formed by lamellae. This is the region of bone called compact bone. Osteons are arranged in parallel to the long axis of the bone. The Haversian canals surround blood vessels and nerve cells throughout the bone and communicate with osteocytes in lacunae (spaces within the dense bone matrix that contain the living bone cells) through canaliculi. This unique arrangement is conducive to mineral salt deposits and storage which gives bone tissue its strength.
An anatomical structure consisting of multiple cell cluster organs, that has a largely bona-fide boundary and that does not contain portions of tissue.
Examples: compound eye; Johnston's organ.
Central region of the telencephalon, located in the pallium. Found in reptiles and birds
The term allocortex refers to one of two types of cerebral cortex defined on the basis of cytoarchitecture and fetal development. The other is neocortex. Allocortex does not pass through a prenatal phase of six-layered structure and has three or four layers in the mature brain ( Schiebler-1999 ). Allocortex has three subtypes: paleocortex, archicortex and periallocortex. This definition differs from that in some older sources, which excluded the olfactory bulb and the accessory olfactory bulb ( Carpenter-1983 ).
The allocortex is composed of hippocampal and olfactory structures, which usually display three-layered organization[Brainspan]
Part of the allocortex defined on the basis of cytoarchitecture. The other two are archicortex and periallocortex. It consists of very thin, primitive cortex with few clearly defined layers. It is distinguished ontogenetically by the fact that it does not develop through a cortical plate. It includes the olfactory bulb, accessory olfactory bulb, olfactory tubercle, septum, prepyriform area and periamygdalar area ( Stephan-1975 ). (adapted from Brain Info)
Paleocortex is present in the parahippocampal gyrus,[1] olfactory bulb, accessory olfactory bulb, olfactory tubercle, piriform cortex, periamygdalar area,[2] anterior olfactory nucleus, anterior perforated substance, and prepyriform area
Agranular cortical structures located next to the allocortex.
Subdivision of pallium that is located is the medial position in vertebrates with an evaginated brain and in the distal position in vertebrates with an everted brain.
The pallium of vertebrates have 3 major divisions, medial, dorsal and lateral, but questions of homology are unresolved.
medial zone of dorsal telencephalic area
area dorsalis telencephali, zona medialis
Subdivision of pallium that is located dorsally.
area dorsalis telencephali, zona dorsalis
dorsal zone of dorsal telencephalic area
Subdivision of pallium that is located laterally.
area dorsalis telencephali, zona lateralis
lateral zone of dorsal telencephalic area
A nucleus located in the dorsal pallium that is present in sharks, skates and rays and extends at some levels to the midline..
Most superficial of the areas of the pallium in the enlarged evaginated telencephalon of hagfishes.
Area directly deep to the P1 area of pallium in hagfishes.
Area directly deep to the P2 area of pallium in hagfishes.
Area directly deep to the P3 area of pallium in hagfishes.
Most deep of the areas of the pallium in the enlarged evaginated telencephalon of hagfishes.
A nuclear complex in the avian telecephalon dorsal to the DVR. The Wulst has telencephalic circuitry similar to the DVR.
interstitial part of hyperpallium apicale
The major telecephalic thalamorecipient zone of the tectofugal visual system in Aves.
The gustatory nucleus is the enlarged rostral portion of the solitary nucleus, which receives taste afferents from the glossopharyngeal nerve and the intermediate nerve ( Carpenter-1983 ).
Brainstem tract formed by the central processes of first-order, trigeminal ganglion neurons that extends from the caudal medulla to the midpons. This tract conveys nociceptive and thermal information from the face to second-order neurons in the spinal nucleus of the trigeminal complex.
An element formed from the fusion of metapodium bones 2, 3 and 4 (i.e. either metatarsals 2-4 or metacarpals 3-4).
An element formed from the fusion of metapodium bones 2, 3 and 4 in the pedal autopod.
The cannon bone of the 3-toed jerboa (jaculus jaculus) is the postnatal fusion of the 3 central metatarsals, which are distinct ossified elements prenatally
Anatomical line that delineates a furrow or depression in an organ or tissue.
The crura of the diaphragm are tendinous structures that extend inferiorly from the diaphragm to attach to the vertebral column.
A crus of diaphragm that is in_the_right_side_of a diaphragm.
A crus of diaphragm that is in_the_left_side_of a diaphragm.
A blood vessel that drains from from an upper eyelid.
A blood vessel that drains from from an eyelid.
An artery that supplies blood to an eyelid.
lateral palpebral branch of ophthalmic artery
The medial palpebral arteries (internal palpebral arteries) are arteries of the head. They are two in number, superior and inferior, arise from the ophthalmic, opposite the pulley of the Obliquus superior.
medial palpebral branch of ophthalmic artery
A neuromere that is part of the presumptive forebrain
A neuromere that is part of the presumptive midbrain
A neuromere that is part of the presumptive spinal cord
A group of cells that may not be contained within macroscopic anatomical boundaries, e.g., A9 dopaminergic cell group; massa intercalata of the amygdala (CUMBO)
A reticuloendothelial system that is part of a liver.
Attached to the posterior border of the hard palate is a thin, firm fibrous lamella called the palatine aponeurosis, which supports the muscles and gives strength to the soft palate. It is thicker above than below, where it becomes very thin and difficult to define. Laterally it is continuous with the pharyngeal aponeurosis. It serves as the insertion for the Tensor veli palatini and Levator veli palatini, and the origin for the Musculus uvulae, Palatopharyngeus, and Palatoglossus. It provides support for the soft palate.
A muscle organ that is part of a cloaca.
a very prominent superficial muscle and with its almost transverse course it forms the boundary between the abdomen and the tail.
a long narrow muscle arising from the underside of feather bulge of the lateral rectrices, inserting near the midline of the cloacal tubercle - phallus.
Extraembryonic part of the vein passing through the umbilical cord to the fetus and returning the purified and nutrient blood from the placenta.
A extraembryonic umbilical vein that is in_the_left_side_of a multicellular organism.
A extraembryonic umbilical vein that is in_the_right_side_of a multicellular organism.
Vein passing through the umbilical cord to the fetus and returning the purified and nutrient blood from the placenta[VHOG:0000400].
The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ.
Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin.
Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin.
A muscle organ that is part of a pectoral appendage (forelimb or pectoral fin).
A muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin).
Organ component cluster which consists of the fusion of the tendons of origin of the four rectus muscles of the eye. Examples: There are only two instances, right and left common tendinous rings.
A jaw muscle that arises from trunk somites and is innervated by spinal nerves.
The most anterior of the trapezius muscles, found in felids, it is also the largest. Its fibers run obliquely to the ventral surface. Its origin is the superior nuchal line and median dorsal line and its insertion is the clavicle. Its action is to draw the clavicle dorsally and towards the head.
Acromiotrapezius is the middle trapezius muscle. It covers the dorsal and lateral surfaces of the scapula. Its origin is the neural spines of the cervical vertebrae and its insertion is in the metacromion process and fascia of the clavotrapezius. Its action is to draw the scapula to the dorsal, and hold the two scapula together.
Spinotrapezius, also called thoracic trapezius, is the most posterior of the three trapezius muscles. It is triangular shaped. Posterior to the acromiotrapezius and overlaps latissimus dorsi on the front. Its origin is the neural spines of the thoracic vertebrae and its insertion is the scapular fascia. Its action is to draw the scapula to the dorsal and caudal regions.
The nuchal lines are four curved lines on the external surface of the occipital bone: The upper, often faintly marked, is named the highest nuchal line, and to it the galea aponeurotica is attached. Below the highest nuchal line is the superior nuchal line. To it is attached the Sternocleidomastoid muscle, Occipitalis muscle, and Splenius capitis muscle, and the trapezius muscle. From the external occipital protuberance a ridge or crest, the median nuchal line, often faintly marked, descends to the foramen magnum, and affords attachment to the ligamentum nuchC&. Running from the middle of this line is the inferior nuchal line. Attached are the Obliquus capitis superior muscle, Rectus capitis posterior major muscle, and Rectus capitis posterior minor muscle.
Of the nuchal lines, the upper, often faintly marked, is named the highest nuchal line, but is sometimes referred to as the Mempin Line, and to it the galea aponeurotica is attached.
Of the nuchal lines, the one below the highest nuchal line is the superior nuchal line. To it is attached the Occipitalis muscle, the Splenius capitis muscle, the trapezius muscle, and the Sternocleidomastoid muscle.
Of the nuchal lines, the one that runs from the external occipital protuberance a ridge or crest is the median nuchal line, often faintly marked, descends to the foramen magnum, and affords attachment to the ligamentum nuchae.
Of the nuchal lines, the one running from the middle of the median line is the inferior nuchal line. Attached are the Obliquus capitis superior muscle, Rectus capitis posterior major muscle, and Rectus capitis posterior minor muscle.
The most superficial of pectoral muscles, found in some mammals
The most deep of pectoral muscles, found in some mammals
A muscle that is important to the body support of limbed reptiles, underlies the front part of the pectoral muscle, arises from the coracoid, and passes to the underpart of the humerus
A dorsal muscle of lower tetrapods that runs from the lumbar region and girdle to the femur.
A ventral muscle of lower tetrapods that runs from the pubis and ischium to the femur.
The Vastus intermedius (Cruraeus) arises from the front and lateral surfaces of the body of the femur in its upper two-thirds, sitting under Rectus Femoris and from the lower part of the lateral intermuscular septum. Its fibers end in a superficial aponeurosis, which forms the deep part of the Quadriceps femoris tendon. The Vastus medialis and Vastus intermedius appear to be inseparably united, but when the Rectus femoris has been reflected a narrow interval will be observed extending upward from the medial border of the patella between the two muscles, and the separation may be continued as far as the lower part of the intertrochanteric line, where, however, the two muscles are frequently continuous.
Origin: anterior and lateral surfaces of femur; insertion: patella, common tendon of quadriceps femoris; innervation: femoral; action, extends leg[BTO:0002542].
A placental membrane that consists of three trophoblast cell layers.
A placental membrane that consists of a single layer of syncytiotrophoblast at term.
Chorda tendinea which is attached to the leaflet of mitral valve and is continuous with the endocardium of papillary muscle of left ventricle.
Chorda tendinea which is attached to the leaflet of tricuspid valve and is continuous with the endocardium of papillary muscle of right ventricle.
Leaflet of mitral valve which is attached to the commissural chorda tendinea of left ventricle.
Leaflet of mitral valve which is attached to the anterior head of the posterior papillary muscle of left ventricle through the chorda tendinea of the left ventricle.
aortic leaflet of the left-sided mitral valve
Leaflet of mitral valve which is attached to the posterior head of the lateral papillary muscle of left ventricle through the chorda tendinea of the left ventricle.
The larval form of any of the Taenia tapeworms.
A crustacean larval stage characterised by the use of the thoracic appendages for swimming.
A crustacean larval stage characterised by the use of abdominal appendages (pleopods) for propulsion.
The crustacean post-larval stage of a crab
A development stage of copepods which follows the nauplius stage. It is segmented with more than 3 pairs of appendages
A developmental stage in a hermit crab that has completed the swimming larval stages.
A larval stage of a trochozoan in which the organism is in free-swimming planktonic form with several bands of cilia[WP,modified].
The characteristic larval stage of the gastropod, bivalve and scaphopod taxonomic classes. It is produced following either the embryonic or trochophore larval stage of development
The larval stage of members of the order Lepidoptera.
The orbital fissure that is situated inferiorly between the greater wing of the sphenoid bone and the maxilla
A distal epiphysis that is part of a distal phalanx of pedal digit 1.
distal epiphysis of distal phalanx of big toe
distal epiphysis of distal phalanx of pedal digit I
head of distal phalanx of first digit of foot
distal epiphysis of distal phalanx of pedal digit 1
A distal epiphysis that is part of a distal phalanx of pedal digit 2.
distal end of distal phalanx of second toe
distal epiphysis of distal phalanx of pedal digit II
distal epiphysis of distal phalanx of second toe
distal epiphysis of distal phalanx of pedal digit 2
A distal epiphysis that is part of a distal phalanx of pedal digit 3.
distal end of distal phalanx of third toe
distal epiphysis of distal phalanx of pedal digit III
distal epiphysis of distal phalanx of third toe
head of distal phalanx of third digit of foot
distal epiphysis of distal phalanx of pedal digit 3
A distal epiphysis that is part of a distal phalanx of pedal digit 4.
distal end of distal phalanx of fourth toe
distal epiphysis of distal phalanx of fourth toe
distal epiphysis of distal phalanx of pedal digit IV
head of distal phalanx of fourth digit of foot
distal epiphysis of distal phalanx of pedal digit 4
A distal epiphysis that is part of a distal phalanx of pedal digit 5.
distal end of distal phalanx of little toe
distal epiphysis of distal phalanx of little toe
distal epiphysis of distal phalanx of pedal digit V
head of distal phalanx of fifth digit of foot
distal epiphysis of distal phalanx of pedal digit 5
distal epiphysis of distal phalanx of pedal digit
A distal epiphysis that is part of a distal phalanx of manual digit 1.
distal epiphysis of distal phalanx of manual digit I
distal epiphysis of distal phalanx of thumb
head of distal phalanx of first digit of hand
distal epiphysis of distal phalanx of manual digit 1
A distal epiphysis that is part of a distal phalanx of manual digit 2.
distal end of distal phalanx of index finger
distal end of distal phalanx of second finger
distal epiphysis of distal phalanx of index finger
distal epiphysis of distal phalanx of manual digit II
distal epiphysis of distal phalanx of manual digit 2
A distal epiphysis that is part of a distal phalanx of manual digit 3.
distal end of distal phalanx of middle finger
distal end of distal phalanx of third finger
distal epiphysis of distal phalanx of manual digit III
distal epiphysis of distal phalanx of middle finger
head of distal phalanx of third digit of hand
distal epiphysis of distal phalanx of manual digit 3
A distal epiphysis that is part of a distal phalanx of manual digit 4.
distal end of distal phalanx of fourth finger
distal end of distal phalanx of ring finger
distal epiphysis of distal phalanx of manual digit IV
distal epiphysis of distal phalanx of ring finger
head of distal phalanx of fourth digit of hand
distal epiphysis of distal phalanx of manual digit 4
A distal epiphysis that is part of a distal phalanx of manual digit 5.
distal end of distal phalanx of fifth finger
distal end of distal phalanx of little finger
distal epiphysis of distal phalanx of little finger
distal epiphysis of distal phalanx of manual digit V
head of distal phalanx of fifth digit of hand
distal epiphysis of distal phalanx of manual digit 5
head of distal phalanx of digit of manus
distal epiphysis of distal phalanx of manual digit
A distal epiphysis that is part of a distal phalanx.
head of distal phalanx of digit of autopod
distal epiphysis of distal phalanx of digit
A muscle in amphibians that connects originates in the ilium and inserts in the tibia.
A cerebellar hemisphere that is in_the_left_side_of a cerebellum.
A cerebellar hemisphere that is in_the_right_side_of a cerebellum.
White matter that is part of a brainstem [Automatically generated definition].
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A muscle structure of invertebrates whose origin and insertion sites are in basal side of the epidermis or structures derived from it. The simplest somatic muscles consist of a single cell and associated extracellular structures.
The muscle that is attached at either end to the cuticle[HAO].
A somatic muscle that consists of one or more somatic muscle myotubes and any associated extracellular structures.
A somatic muscle that consists of one or more obliquely striated muscle cells and any associated extracellular structures.
In those cases in which the interilial region is broadly expanded and the pubis is extremely reduced, the anterior margin of the ischium forms an expanded area.
A ligament on the lateral aspect of the human knee, anterior to the fibular collateral ligament.
capsulo-osseous layer of the iliotibial band
A portion of tissue that will develop into vasculature.
A vein receiving blood from adjacent bronchopulmonary segments; it emerges from the inferior margin of a segment to become a tributary of a branch of a pulmonary vein.
partes intersegmentales venarum pulmonum
One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites.
Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4].
Junction between the cerebellum and the pons.
Part of the forebrain that is ventral to the ventral thalamus and dorsal to the preoptic area. See page 44 of the Atlas of Early Zebrafish Brain Development[UBERON:2007010, ZFIN:curator].
The pallial region located next to the pallium-subpallium boundary.
A barrier between the blood or haemolymphatic fluid and the testes.
The bend in the facial nerve at the lateral end of the internal acoustic meatus.
On of a pair of medial protrusions of the intra-pharyngeal ostium (an oval opening within the soft palate that connects the oral and nasal portions of the pharynx), used in vocalization in Koalas.
Muscle notes: Because the larynx is attached to the caudal end of the pharynx where the IPO is situated, laryngeal retraction brought about by the sternothyroid muscle will automatically put tension on the rostro-caudally oriented velar vocal folds, and could also induce length changes of the folds. Contractions of the palatopharyngeal muscles may also influence the length and shape of the velar vocal folds directly (inducing width changes of the IPO).
A sphincter muscle that is part of a pouch. The pouch sphincter serves to keep the young from falling out.
The space between a blood vessel and the pia mater.
VRS belonging to the subarachnoid space are continuous with VRS of the subpial space. The direct communication between VRS of the subarachnoid space and the subpial space is unique to the brain’s arteries, as no leptomeningeal layers surround the brain’s veins[WP]
developing superficial cortical layer located just under the pia matter, develops from the marginal layer of the neural tube and becomes cortical layer I
in humans develops into cortical layer I
EMAPA temporally divides this into zone and layer. TODO - unify this with marginal layers in EHDAA2
these layers primarily refer to the mammalian future neocortex
The part of the neocortex hich mainly consists of parts of cingulate, parahippocampal and temporopolar cortice. As distinct from isocortex (typical neocortex) which contains other regions.
A radius bone or its cartilage or pre-cartilage precursor.
A radius-ulna bone or its cartilage or pre-cartilage precursor.
A ulna bone or its cartilage or pre-cartilage precursor.
A tibia bone or its cartilage or pre-cartilage precursor.
A vertebra bone or its cartilage or pre-cartilage precursor.
A vertebral endochondral element in the cervical region of the vertebral column.
A vertebral endochondral element in the thoracic region of the vertebral column.
A lumbar vertebra bone or its cartilage or pre-cartilage precursor.
A vertebra endochondral element that is part of the sacral region of the vertebral column.
A tibiotarsus bone or its cartilage or pre-cartilage precursor.
A tarsometatarsus bone or its cartilage or pre-cartilage precursor.
A fibula bone or its cartilage or pre-cartilage precursor.
A calcaneum bone or its cartilage or pre-cartilage precursor.
A supraoccipital bone or its cartilage or pre-cartilage precursor.
A stapes bone or its cartilage or pre-cartilage precursor.
A incus bone or its cartilage or pre-cartilage precursor.
A malleus bone or its cartilage or pre-cartilage precursor.
A rib bone or its cartilage or pre-cartilage precursor.
Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals.
obsolete otic capsule endochondral element
A forelimb bone or its cartilage or pre-cartilage precursor.
A hindlimb bone or its cartilage or pre-cartilage precursor.
A phalanx bone or its cartilage or pre-cartilage precursor.
A manual digit phalanx bone or its cartilage or pre-cartilage precursor.
manual digit phalanx endochondral element
A manual digit 1 phalanx bone or its cartilage or pre-cartilage precursor.
manual digit I phalanx endochondral element
manual digit 1 phalanx endochondral element
A manual digit 2 phalanx bone or its cartilage or pre-cartilage precursor.
manual digit II phalanx endochondral element
manual digit 2 phalanx endochondral element
A manual digit 3 phalanx bone or its cartilage or pre-cartilage precursor.
manual digit III phalanx endochondral element
manual digit 3 phalanx endochondral element
A manual digit 4 phalanx bone or its cartilage or pre-cartilage precursor.
manual digit IV phalanx endochondral element
manual digit 4 phalanx endochondral element
A manual digit 5 phalanx bone or its cartilage or pre-cartilage precursor.
manual digit V phalanx endochondral element
manual digit 5 phalanx endochondral element
A pedal digit phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit phalanx endochondral element
A pedal digit 1 phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit I phalanx endochondral element
pedal digit 1 phalanx endochondral element
A pedal digit 2 phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit II phalanx endochondral element
pedal digit 2 phalanx endochondral element
A pedal digit 3 phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit III phalanx endochondral element
pedal digit 3 phalanx endochondral element
A pedal digit 4 phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit IV phalanx endochondral element
pedal digit 4 phalanx endochondral element
A pedal digit 5 phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit V phalanx endochondral element
pedal digit 5 phalanx endochondral element
A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit metatarsal endochondral element
A pedal digit 1 metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit 1 metatarsal skeletal element
pedal digit I metatarsal endochondral element
pedal digit 1 metatarsal endochondral element
A pedal digit 2 metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit 2 metatarsal skeletal element
pedal digit II metatarsal endochondral element
pedal digit 2 metatarsal endochondral element
A pedal digit 3 metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit 3 metatarsal skeletal element
pedal digit III metatarsal endochondral element
pedal digit 3 metatarsal endochondral element
A pedal digit 4 metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit 4 metatarsal skeletal element
pedal digit IV metatarsal endochondral element
pedal digit 4 metatarsal endochondral element
A pedal digit 5 metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit 5 metatarsal skeletal element
pedal digit V metatarsal endochondral element
pedal digit 5 metatarsal endochondral element
A manual digit metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit metacarpus skeletal element
manual digit metacarpus endochondral element
A manual digit 1 metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit 1 metacarpus skeletal element
manual digit I metacarpus endochondral element
manual digit 1 metacarpus endochondral element
A manual digit 2 metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit 2 metacarpus skeletal element
manual digit II metacarpus endochondral element
manual digit 2 metacarpus endochondral element
A manual digit 3 metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit 3 metacarpus skeletal element
manual digit III metacarpus endochondral element
manual digit 3 metacarpus endochondral element
A manual digit 4 metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit 4 metacarpus skeletal element
manual digit IV metacarpus endochondral element
manual digit 4 metacarpus endochondral element
A manual digit 5 metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit 5 metacarpus skeletal element
manual digit V metacarpus endochondral element
manual digit 5 metacarpus endochondral element
A basioccipital bone or its cartilage or pre-cartilage precursor.
A carpus bone or its cartilage or pre-cartilage precursor.
A tarsus bone or its cartilage or pre-cartilage precursor.
A exoccipital bone or its cartilage or pre-cartilage precursor.
A femur bone or its cartilage or pre-cartilage precursor.
A humerus bone or its cartilage or pre-cartilage precursor.
A iliac bone or its cartilage or pre-cartilage precursor.
A pubic bone or its cartilage or pre-cartilage precursor.
A ischial bone or its cartilage or pre-cartilage precursor.
A scapula bone or its cartilage or pre-cartilage precursor.
A alisphenoid bone or its cartilage or pre-cartilage precursor.
A orbitosphenoid bone or its cartilage or pre-cartilage precursor.
A sphenoid bone or its cartilage or pre-cartilage precursor.
A limb bone or its cartilage or pre-cartilage precursor.
A delimited region of osteoblasts representing the early stages of bone formation.
A endochondral element that is part of a autopod region.
A autopod endochondral element that is composed primarily of a cartilage tissue.
Endochondral element located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE].
A distal mesopodial endochondral element that is part of a forelimb.
A distal carpal endochondral element that is composed primarily of a cartilage tissue.
A centrale endochondral element that is composed primarily of a cartilage tissue.
A proximal mesopodial endochondral element that is part of a forelimb.
A proximal carpal endochondral element that is composed primarily of a cartilage tissue.
A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation.
proximal carpal bone pre-cartilage condensation
A proximal mesopodial endochondral element that is part of a hindlimb.
A proximal tarsal endochondral element that is composed primarily of a cartilage tissue.
A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation.
proximal tarsal bone pre-cartilage condensation
distal carpal bone 1 endochondral element
A distal carpal bone 1 endochondral element that is composed primarily of a cartilage tissue.
A distal carpal bone 1 endochondral element that is composed primarily of a pre-cartilage condensation.
distal carpal bone 1 pre-cartilage condensation
distal carpal bone 2 endochondral element
A distal carpal bone 2 endochondral element that is composed primarily of a cartilage tissue.
A distal carpal bone 2 endochondral element that is composed primarily of a pre-cartilage condensation.
distal carpal bone 2 pre-cartilage condensation
distal carpal bone 3 endochondral element
A distal carpal bone 3 endochondral element that is composed primarily of a cartilage tissue.
A distal carpal bone 3 endochondral element that is composed primarily of a pre-cartilage condensation.
distal carpal bone 3 pre-cartilage condensation
distal carpal bone 4 endochondral element
A distal carpal bone 4 endochondral element that is composed primarily of a cartilage tissue.
A distal carpal bone 4 endochondral element that is composed primarily of a pre-cartilage condensation.
distal carpal bone 4 pre-cartilage condensation
distal carpal bone 5 endochondral element
A distal carpal bone 5 endochondral element that is composed primarily of a cartilage tissue.
A distal carpal bone 5 endochondral element that is composed primarily of a pre-cartilage condensation.
distal carpal bone 5 pre-cartilage condensation
A distal mesopodial endochondral element that is part of a hindlimb.
A distal tarsal endochondral element that is composed primarily of a cartilage tissue.
A distal tarsal endochondral element that is composed primarily of a pre-cartilage condensation.
distal tarsal bone pre-cartilage condensation
distal tarsal bone 1 endochondral element
A distal tarsal bone 1 endochondral element that is composed primarily of a cartilage tissue.
A distal tarsal bone 1 endochondral element that is composed primarily of a pre-cartilage condensation.
distal tarsal bone 1 pre-cartilage condensation
distal tarsal bone 2 endochondral element
A distal tarsal bone 2 endochondral element that is composed primarily of a cartilage tissue.
A distal tarsal bone 2 endochondral element that is composed primarily of a pre-cartilage condensation.
distal tarsal bone 2 pre-cartilage condensation
distal tarsal bone 3 endochondral element
A distal tarsal bone 3 endochondral element that is composed primarily of a cartilage tissue.
A distal tarsal bone 3 endochondral element that is composed primarily of a pre-cartilage condensation.
distal tarsal bone 3 pre-cartilage condensation
distal tarsal bone 4 endochondral element
A distal tarsal bone 4 endochondral element that is composed primarily of a cartilage tissue.
A distal tarsal bone 4 endochondral element that is composed primarily of a pre-cartilage condensation.
distal tarsal bone 4 pre-cartilage condensation
distal tarsal bone 5 endochondral element
A distal tarsal bone 5 endochondral element that is composed primarily of a cartilage tissue.
A distal tarsal bone 5 endochondral element that is composed primarily of a pre-cartilage condensation.
distal tarsal bone 5 pre-cartilage condensation
The remnant of the lamina terminalis in the developed brain.
In the developed brain, the lamina terminalis remains as the thin rostral wall of the third ventricle, stretching from the bases of the major cerebral commissures (the anterior commissure, the commissure of the fornix, and the rostrum of the corpus callosum) to the dorsal surface of the optic chiasm[MGI:anna]
lamina terminalis of cerebral hemisphere
A group of neurons in the cortex of the brain which can be successively penetrated by a probe inserted perpendicularly to the cortical surface, and which have nearly identical receptive fields.
The anterior organ of a tapeworm used for attachment to the host intestine.
A outer canthus that is in_the_right_side_of a head.
A outer canthus that is in_the_left_side_of a head.
An anatomical line of the face that connects the two outer (lateral) canthi of the eye. The length of this line is known as the outer canthal distance.
Internodal tract which consists of the atrial and atrial septal branches.
posterior internodal tract muscle tissue
perimysial connective tissue of subepicardium
A adipose tissue that is part of a epicardium.
A connective tissue that is part of a prostate gland.
subepithelial connective tissue of prostatic gland
The tapering portion of the gall bladder that narrows to form the neck and cystic duct.
A large fat pad that is located at the base of the abdominal wall, in the falciform ligament of the liver.
Encapsulated adipose tissue associated with the mesentery
A strand of hair that is part of a autopod region.
A strand of hair that is part of a manus.
A strand of hair that is part of a pinna.
A strand of hair that is part of a tail.
A strand of hair that is part of a ventrum.
A strand of hair that is part of a dorsum.
A duct that is part of a Harderian gland. opens into the conjunctival sac at the base of the nictitating membrane.
Typically a single duct per gland, but Harderian glands can have more than 1 duct, e.g. in lizards, amphisbaenids and primitive snakes (Bellairs & Boyd, 1947) and possibly some avian species (Burns, 1992)
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
A gland that is located in the ocular region, nearer the inner canthi. Typically associated with or part of the nictitating membrane, when present
Rabbits, pigs and Mongolian gerbils have both a Harderian and a nictitans gland[ISBN:1118473523]
the distinction between Harderian and nictitans gland is only valid in mammals - the medial ocular glands in other terapods are called Harderian glands regardless of their secretion[doi:10.1007/978-3-642-76685-5_2]
A gland that is located in or around the ocular region, nearer the outer canthi.
The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104
A anatomical space that is enclosed by a conjunctiva.
The two terminal branches of the ophthalmic artery in humans are the dorsal nasal artery and the supratrochlear artery
The middle temporal artery occasionally gives off a zygomatico-orbital branch, which runs along the upper border of the zygomatic arch, between the two layers of the temporal fascia, to the lateral angle of the orbit. This branch, which may arise directly from the superficial temporal artery, supplies the Orbicularis oculi, and anastomoses with the lacrimal and palpebral branches of the ophthalmic artery.
The blood supply to the (Harderian) gland has been reported in greatest detail in the sparrow Passer domesticus (Slonaker, 1918), where it is derived through the ophthalmotemporal branch of the external ophthalmic artery http://www.ncbi.nlm.nih.gov/pubmed/7559104
ophthalmotemporal branch of external ophthalmic artery
The supraorbital artery is an artery of the head. It springs from the ophthalmic artery as that vessel is crossing over to the medial side of the optic nerve.
supraorbital branch of external ophthalmic artery
The inferior branch of the oculomotor nerve or the inferior division, the larger, divides into three branches. One passes beneath the optic nerve to the medial rectus. Another, to the inferior rectus. The third and longest runs forward between the inferior recti and lateralis to the inferior oblique. From the last a short thick branch is given off to the lower part of the ciliary ganglion, and forms its short root. All these branches enter the muscles on their ocular surfaces, with the exception of the nerve to the inferior oblique, which enters the muscle at its posterior border.
ramus inferior (nervus oculomotorius [III])
The superior branch of the oculomotor nerve or the superior division, the smaller, passes medialward over the optic nerve. It supplies the Superior rectus and Levator palpebrae superioris.
ramus superior (nervus oculomotorius [III])
An eye consisting of multiple light-sensing organs
Light reflecting layer found in a variety of different types of eye.
An eye that consists of a cluster of three or four ➞median eyes that form a single structural unit but are separated from one another by pigment layers
A corkscrew-like artery in premenstrual or progestational endometrium; uterine spiral arteries play a vital role in supplying nutrients to the placenta and fetus, and are thus remodeled into highly dilated inelastic vessels by the action of invading trophoblast (physiological change)
In women, rats and mice, the endometrial vessels are coiled and known as spiral arteries[PMID:16413937].
A blood vessel that is part of a endometrium.
The helicine branches of uterine artery (or helicine arterioles, or spiral arteries) are small arteries which temporarily supply the endometrium of the uterus during the luteal phase of the menstrual cycle. In histology, identifying the presence of these arteries is one of the most useful techniques in identifying the phase of the cycle.
Notes: The straight branches of the radial arteries of the uterus terminate in capillaries in the basal layer, while the spiral or coiled branches penetrate to the surface epithelium
The helicine arteries of penis are arteries in the penis. They are found in the corpora cavernosa penis. They are involved in the process of erection.
Either the helicine artery of the penis or the helicine artery of the uterus
A region of somite adjacent to presomitic mesoderm.
Epithelium located in the intersomitic region.
The neck of talus is directed forward and medialward, and comprises the constricted portion of the bone between the body and the oval head. Its upper and medial surfaces are rough, for the attachment of ligaments; its lateral surface is concave and is continuous below with the deep groove for the interosseous talocalcaneal ligament.
The slightly constricted part of a tooth, between the crown and the root.
The capillary bed that initially surrounds the relative avascular brain and spinal cord; the perineural vascular plexus (PNVP) is the precursor to the blood brain barrier formed by angioblasts which migrate away from somites and is recruited to surround the neural tube in response to VEGF; vascularization of the brain and spinal cord occurs via angiogenesis as sprouting vessels from the PNVP invade the neuroepithelium and grow inward toward the ventricular lumen[MP].
A circulatory organ that is reponsible for pumping lymph throughout the body.
An anatomical group whose component structures share a common function.
A non-connected functional system that is composed primarily of a gland.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
Typical barnacles, common name of the sedentary crustacean marine animals constituting the subclass Cirripedia, attach to the substrate by means of an exceedingly adhesive cement, produced by a cement gland, and secrete a shell, or carapace, of calcareous (limestone) plates, around themselves.
The median arcuate ligament is a ligament under the diaphragm that connects the right and left crura of diaphragm.
The middle meatus is a nasal opening or canal situated between the middle and inferior conchae, and extends from the anterior to the posterior end of the latter. The lateral wall of this meatus can be satisfactorily studied only after the removal of the middle concha. On it is a curved fissure, the hiatus semilunaris, limited below by the edge of the uncinate process of the ethmoid and above by an elevation named the bulla ethmoidalis; the middle ethmoidal cells are contained within this bulla and open on or near to it. Through the hiatus semilunaris the meatus communicates with a curved passage termed the infundibulum, which communicates in front with the anterior ethmoidal cells and in rather more than fifty percent of skulls is continued upward as the frontonasal duct into the frontal air-sinus; when this continuity fails, the frontonasal duct opens directly into the anterior part of the meatus. Below the bulla ethmoidalis and hidden by the uncinate process of the ethmoid is the opening of the maxillary sinus (ostium maxillare); an accessory opening is frequently present above the posterior part of the inferior nasal concha.
The inferior meatus, the largest of the three meatuses of the nose, is the space between the inferior concha and the floor of the nasal cavity. It extends almost the entire length of the lateral wall of the nose, is broader in front than behind, and presents anteriorly the lower orifice of the nasolacrimal canal.
The ventral nasal meatus is found between the ventral nasal concha and the dorsal surface of the hard palate.It connects the nasal vestibule with the nasopharynx. Rostrally it is narrow at the nasal vestibule and widens caudally towards the nasopharyngeal meatus. The ventral nasal meatus is the main passage for air. Apart from olfaction, the nasal cavity functions to warm the inhaled air as it passes through the meatuses over the vascular beds of the mucosa. The air is humidified by the vaporization of tears and serous nasal secretion. The air is cleaned throughout the scattered mucous glands. These glands secrete mucous through the nasal cavity and the mucous serves to trap the large particles that come into contact with it. PPP Clinically in the horse the ventral nasal meatus is the main passage through which a stomach tube can be passed to the pharynx and oesophagus and then to the stomach. This kind of a tube is commonly used when drenching a horse for colic, as well as having many other veterinary applications. The tube has to pass through the ventral nasal meatus to the nasopharyngeal meatus and the caudal nares to reach the pharynx and oesophagus. If the tube is accidentally passed into the dorsal or middle nasal meatuses it would pass to the ethmotubinates and cause massive haemorrhage.
The dosal nasal meatus is a narrow passage bounded dorsally by the roof of the nasal cavity and ventrally by the dorsal concha. It terminates caudally at the junction of the inner plate of the frontal bone with the cribiform plate and lateral mass of the ethmoid bone. It is the shortest and shallowest of the three meatuses.
A anatomical conduit that is part of a ventricular septum intermedium.
A anatomical conduit that is part of a atrial septum intermedium.
A vessel down which passes a wave of muscular contraction, that forces the flow of haemolymphatic fluid.
See http://www.ncbi.nlm.nih.gov/pubmed/20235196 for discussion of whether embryonic vertebrate heart is peristaltic
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
The feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine.
A nucleus of brain that is part of a dorsal thalamus.
A nucleus of brain that is part of a ventral thalamus.
A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals.
An unpaired left-sided accessory organ which plays a role in establishing lateral brain left right asymmetry[ZFA:0001360, ZFIN:ZDB-PUB-030206-1].
In lampreys and apparently in some fossil fish, the parapineal body and the pineal body (epiphysis) are a bilateral pair of structures rather than being located in series, one in front of the other. A pair of visual structures may have been the ancestral condition of this pineal complex (Weichert, 1970, p.622). The parapineal organs of lampreys, tadpoles, and lizards possess cells similar to rods and cones. Frogs possess a brow spot or frontal organ where ancestral pineal eye might have been (Weichert, 1970, p.622)
accessory olfactory bulb, granular layer
A spatially segregated cluster of sensory cells in the nasal cavity.
A small island of olfactory neuroepithelium lying bilaterally at the ventral base of the nasal septum near the entrance of the nasopharynx.
This olfactory apparatus has been observed in many mammals, including rat, mouse, hamster, deer mouse, rabbit, opossum, guinea pig, bandicoot, and koala (Rodolfo-Masera 1943; Adams and McFarland 1971; Bojsen-Moller 1975; Katz and Merzel 1977; Breipohl et al. 1983, 1989; Kratzing 1984a, 1984b; Taniguchi et al. 1993), but not in cat (Breipohl et al. 1983) or ferret (Weiler and Farbman 2003)
This is the point at which the trachea splits into two (left and right) principal bronchi. It is located in the region of the fourth to sixth intercostal space, though this varies with species and with respiratory phase. This position closely associates the bifurcation with the heart base. The thickened median crest initiating the bifurcation is called the tracheal carina .
A zone of skin that is part of a digit [Automatically generated definition].
A hair follicle that is part of a coat of hair.
A pancreatic lobule that is in_the_left_side_of a exocrine pancreas.
A pancreatic lobule that is in_the_right_side_of a exocrine pancreas.
A basement membrane of epithelium that is part of a respiratory system.
A branch of the descending genicular artery, the last branch (most distal) of the femoral, the saphenous is also variable. It usually lies between the sartorius and the garcilis muscles and supplies their distal ends. The artery accompanies the saphenous nerve. It usually supplies the skin on the medial and proximal part of the leg. The artery may continue to join, in varying degrees, the dorsalis pedis artery and plantaris pedis arteries.
The segment of either hepatic duct located in the hilum of the liver.
Muscle organ located on the dorsal surface of the head innervated by the facial nerve
accessory olfactory bulb mitral cell layer
A thin layer of fibrous tissue capable of stretching and contracting. It is part of the tunica media of the blood vessels.
A duct that is part of a anterior lingual gland.
A lymph node that is part of a hypodermis.
A fat pad that is part of a mediastinum.
The splenic lymph nodes (or pancreaticolienal) accompany the lienal (splenic) artery, and are situated in relation to the posterior surface and upper border of the pancreas; one or two members of this group are found in the gastrolienal ligament. Their afferents are derived from the stomach, spleen, and pancreas, their efferents join the celiac group of preaortic glands.
A lymph node located near the bifurcation of the trachea.
Single (unpaired) lymph node at the tracheal bifurcation.
A zone of skin that is part of a axilla.
A zone of skin that is part of a external nose.
A zone of skin that is part of a scrotum.
The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery.
A hepatic artery that is part of a left lobe of liver.
A hepatic artery that is part of a right lobe of liver.
A zone of skin that is part of a metapodial pad.
hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla.
The sural nerve (short saphenous nerve), formed by the junction of the medial sural cutaneous with the peroneal anastomotic branch of the lateral sural cutaneous nerve, passes downward near the lateral margin of the tendo calcaneus, lying close to the small saphenous vein, to the interval between the lateral malleolus and the calcaneus. It runs forward below the lateral malleolus, and is continued as the lateral dorsal cutaneous nerve along the lateral side of the foot and little toe (via a dorsal digital nerve), communicating on the dorsum of the foot with the intermediate dorsal cutaneous nerve, a branch of the superficial peroneal. In the leg, its branches communicate with those of the posterior femoral cutaneous.
An area within the corpus callosum, a white matter structure within the cleft that separates the left and right cerebral hemispheres in the mammalian brain, between the genu (anterior region) and the splenium (posterior region).
A gyrus that is part of a frontal cortex.
Part of corpus callosum comprising the "kneelike" anterior bend (adapted from Nolte, The Human Brain, 6th ed., 2009 pg 664)
The part of the corpus callosum that projects posteriorly and inferiorly from the anteriormost genu.
Either the inferior or superior sagittal sinus
The posterior end of the corpus callosum. It overlaps the tela chorioidea of the third ventricle and the mid-brain, and ends in a thick, convex, free border.
A epithelium that is part of a anal canal.
A smooth muscle tissue that is part of a ejaculatory duct.
smooth muscle tissue layer of ejaculatory duct
A smooth muscle tissue that is part of a inferior eyelid tarsus.
Multilaminar epithelium, which consists of more than one layer of cuboidal and columnar cells, only one layer of which is in contact with a basement membrane. Examples: epithelium of wall of pancreatic duct, epithelium of wall of duct of salivary gland.
mixed stratified cuboidal and columnar epithelium
Regular connective tissue, which consists of fibroblasts and of intercellular matrix, which contains elastic fiber bundles oriented predominantly in definable directions.
A epithelium that is part of a duct of salivary gland.
transitional epithelium of prostatic urethra
A smooth muscle tissue that is part of a hypodermis.
muscle layer in fatty layer of subcutaneous tissue
smooth muscle layer in fatty layer of subcutaneous tissue
A duct that is part of a olfactory gland.
A acinus that is part of a olfactory gland.
The portion of the nasal mucosa that is part of the respiratory system.
lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose.
Any anatomical conduit which is part of the upper respiratory tract
Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132].
An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper
A zone of skin that is part of a autopod region.
A connective tissue that is part of a digit.
Thin layer of cortex lying on the dorsal surface of the corpus callosum. It has been debated whether it is more related to the hippocampus or the olfactory bulb (Shipley et al., Olfactory System In Paxinos The Rat Nervous System, 2nd ed)
A epithelium that is part of a lobar bronchus of left lung.
A epithelium that is part of a lobar bronchus of right lung.
A continuation ventrally of the supracallosal gyrus beyond the rostrum of the corpus callosum. It is demonstrated histologically by Nissl stain. In the human ( Anthoney-1994 ) and the macaque ( Paxinos-2004 ) it lies on the rostral surface of the lamina terminalis and is considered identical to or part of the paraterminal gyrus. In the rat ( Swanson-1998 ) and the mouse ( Paxinos-2001 ) it is located similarly in relation to the supracallosal gyrus, however, it is a more prominent layered structure that extends rostrally on the medial surface overlying the anterior olfactory nucleus. It is considered part of the olfactory areas (rodent) of the cerebral cortex. In rodents it consists of two parts, the dorsal tenia tecta and the ventral tenia tecta. Note that some authors use the term 'tenia tecta' or 'taenia tecta' as a synonym for the lateral longitudinal stria ( Riley-1943 ).
A epithelium that is part of a camera-type eye.
A epithelium that is part of a middle ear.
A epithelium that is part of a external ear.
TODO - disambiguate between developing and adult structure
A lamina propria that is part of a duodenum.
A dental pulp that is part of a incisor tooth.
FMA has classes for very specific sublcasses but no generic grouping at this level
A dental lamina that is part of a incisor tooth.
A tooth enamel organ that is part of a incisor tooth.
A odontogenic mesenchyme that is part of a incisor tooth.
A upper jaw incisor that is in_the_left_side_of a dentition.
An incisor tooth that protrudes beyond the mouth.
An cuspid tooth that protrudes beyond the mouth.
A upper jaw incisor that protrudes prominently from the mouth as a single median tusk, found in narwhals.
A dental pulp that is part of a narwhal tusk.
An anatomical line that connects two successive vertebral pedicles. The length of this line is known as the interpedicular distance.
A thickening of the surface ectoderm on the ventral side of the embryonic tail which resembles the apical ectodermal ridge of the limb bud.
A group of ectodermal cells that serves as an important signaling center in the mouse tail-bud following completion of gastrulation, and contains progenitor cells that contribute to the ventral midline ectoderm of the tail; ablation of the VER leads to defects in somitogenesis and tail elongation[MP]
A lymph node found near the parotid gland.
Any of the lymph nodes adjacent to the stomach and duodenum.
A lymph node along the left gastric artery or greater omentum.
Single (unpaired) lymph node in the lesser omentum at the minor curvature of the stomach
lymph nodes of the pancreatic tail and spleen, receiving afferents from both organs plus the greater curvature of the stomach; they drain to the celiac lymph nodes.
Consider obsoleting - this is apparently an obsolete term that regarded the pancreatic and splenic lymph nodes as a single anatomic unit.[http://medical-dictionary.thefreedictionary.com/pancreaticosplenic+lymph+nodes]
lymph node of anterior border of epiploic foramen
lymph node of anterior border of omental foramen
node of anterior border of epiploic foramen
node of anterior border of omental foramen
The retropharyngeal lymph nodes, from one to three in number, lie in the buccopharyngeal fascia, behind the upper part of the pharynx and in front of the arch of the atlas, being separated, however, from the latter by the Longus capitis. Their afferents drain the nasal cavities, the nasal part of the pharynx, and the auditory tubes. Their efferents pass to the superior deep cervical glands. They are in the retropharyngeal space.
The mandibular lymph node is a lymph node found near the jaw.
In mice, Rostromedial to the sublingual and mandibular salivary glands.
The part of the foot that is the projection of the calcaneus.
Any lymph node within the abdominal pelvic region.
The external iliac lymph nodes, from eight to ten in number, lie along the external iliac vessels. They are arranged in three groups, one on the lateral, another on the medial, and a third on the anterior aspect of the vessels; the third group is, however, sometimes absent. Their principal afferents are derived from the inguinal lymph nodes, the deep lymphatics of the abdominal wall below the umbilicus and of the adductor region of the thigh, and the lymphatics from the glans penis vel clitoridis, the membranous urethra, the prostate, the fundus of the urinary bladder, the cervix uteri, and upper part of the vagina.
One of the deep inguinal lymph nodes located in or adjacent to the femoral canal; sometimes mistaken for a femoral hernia when enlarged.
nodus lymphoideus inguinalis profundi proximalis
The term tonsillar node can be inaccurate or ambiguous
Dorsolateral to the mandibular lymph node.
Rostromedial to the sublingual and mandibular salivary glands Dorsolateral to the mandibular lymph node Ventral to the external acoustic pore, caudal to the extraorbital lacrimal gland, cranioventral to the parotid salivary gland, dorsal to the junction between the superficial temporal vein (v.) and the maxillary v..
Medial to the external jugular vein and sternocephalic muscle (m.), lateral to sternohyoid m., caudal to digastric m., dorsal to the trachea.
A lymph node that is medial to the gluteus superficialis m., caudal to gluteus medius m. and sciatic nerve lymph node
The mastoid lymph nodes (retroauricular lymph nodes, posterior auricular glands), usually two in number, are situated on the mastoid insertion of the Sternocleidomastoideus, beneath the Auricularis posterior. Their afferent vessels drain the posterior part of the temporoparietal region, the upper part of the cranial surface of the auricula or pinna, and the back of the external acoustic meatus; their efferents pass to the superior deep cervical glands.
The preauricular deep parotid lymph nodes (anterior auricular glands or preauricular glands), from one to three in number, lie immediately in front of the tragus. Their afferents drain the lateral surface of the auricula and the skin of the adjacent part of the temporal region; their efferents pass to the superior deep cervical glands.
The infra-auricular deep parotid lymph nodes are a group of lymph nodes found underneath the ear.
The submental lymph nodes (or suprahyoid) are situated between the anterior bellies of the Digastrici. Their afferents drain the central portions of the lower lip and floor of the mouth and the apex of the tongue. Their efferents pass partly to the submandibular lymph nodes and partly to a gland of the deep cervical group situated on the internal jugular vein at the level of the cricoid cartilage.
A lymph node that is part of a hindlimb.
A lymph node that is part of a forelimb.
The infrapatellar fat pad, also known as Hoffa's fat pad, is a cylindrical piece of fat that is situated under and behind the patella bone within the knee.
Single (unpaired) lymph node in the mesoduodenum, dorsal to the portal vein, surrounded by pancreatic tissue
In the mesocolon at the transition between ascending colon and transverse colon
The thoracic wall (or chest wall) is the boundary of the thoracic cavity. The bony portion is known as the thoracic cage. However, the wall also includes muscle, skin, and fascia.
Subdivision of chest wall which includes the ribcage, muscle group of thoracic wall and costal pleura. Examples: There is only one thoracic wall[FMA:10428].
A vertebral arch joint that is part of a cervical region of vertebral column.
joint of cervical vertebral articular process
zygapophyseal joint of cervical vertebrae
zygapophysial joint of cervical vertebrae
The circumference of the base of the glans forms a rounded projecting border, the corona of the glans penis, overhanging a deep retroglandular sulcus, behind which is the neck of the penis.
A breast that is part of a male organism.
central part of body of bony vertebral centrum
Subdivision of thorax which is anterior to the plane of the posterior boundary of the middle mediastinum.
The nasion (nDb2zD C$nb2) is the intersection of the frontal and two nasal bones of the human skull. Its manifestation on the visible surface of the face is a distinctly depressed area directly between the eyes, just superior to the bridge of the nose.
A compact bone tissue that is part of a bone tissue of long bone.
A compact bone tissue that is part of a diaphysis.
A epiphyseal plate that is part of a radius bone.
proximal interphalangeal joint of little finger
palmar branch of anterior interosseous nerve
Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall.
The glabella is the space between the eyebrows and above the nose. It is slightly elevated, and joins the two superciliary ridges. The term is derived from the Latin 'glabellus', meaning smooth, as this area is usually hairless. The expression of the axial lobe in the cephalon of a trilobite is also referred to as the glabella. The glabella can be used to measure skin turgor in patients suspected of being dehydrated.
A strand of hair that is part of a head.
A strand of hair that is part of a trunk.
maxillary central permanent incisor tooth
maxillary central secondary incisor tooth
maxillary lateral secondary incisor tooth
A hole in the diaphragm through which the esophagus passes
the central point on the posterior surface of the lens.
A zone of skin in the periorbital region of the face.
The midline prominence of the nose, extending from the nasal root to the tip.
On the pinna, a curved prominence of cartilage, parallel with and in front of the helix, is called the antihelix, also known as the anthelix; this divides above into two crura, the crura antihelicis, between which is a triangular depression, the fossa triangularis.
The antitragus is a feature of human ear anatomy. It is a small tubercle that points anteriorly. It is separated from the tragus by the intertragic notch.
A zone of skin that is part of a forehead.
A incisor tooth that is part of a primary dentition.
The zygomatic process of the maxilla (malar process) is a rough triangular eminence, situated at the angle of separation of the anterior, zygomatic, and orbital surfaces. In front it forms part of the anterior surface. Behind it is concave, and forms part of the infratemporal fossa. Above it is rough and serrated for articulation with the zygomatic bone. Below it presents the prominent arched border which marks the division between the anterior and infratemporal surfaces.
A collagenous capsule covering the external surface of the liver.
It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells.
A lymph node that is part of a bronchus.
A soft, thin film of food debris, mucin, and dead epithelial cells deposited on the teeth, providing the medium for the growth of various bacteria. The main inorganic components are calcium and phosphorus, with small amounts of magnesium, potassium, and sodium; the organic matrix consists of polysaccharides, proteins, carbohydrates, lipids, and other components. Plaque plays an important etiologic role in the development of dental caries and periodontal and gingival diseases and provides the base for the development of materia alba; calcified plaque forms dental calculus.
is the sensory system for the sense of hearing.
Auditory system is general anatomical term in FMA
Skeletal element that functionally replaces the notochord[VSAP,modified].
Skeletal element that surrounds the notochord.[VSAO]
the main cylindrical portion of the vertebra ventral to the vertebral canal
The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.
A foramen in the sphenoid bone through which the middle meningeal artery, middle meningeal vein, and the meningeal branch of the mandibular nerve pass.
The palmaris longus is seen as a small tendon between the flexor carpi radialis and the flexor carpi ulnaris, although it is not always present. The muscle is absent in about 14 percent of the population, however this varies greatly with ethnicity. Absence of palmaris does not have any known effect on grip strength. Palmaris longus can be palpated by touching the pads of the fifth and first fingers and flexing the wrist. The tendon, if present, will be very visible.
The juncture where the intestine empties into the cloaca.
Sphincter at the junction of the esophagus and pneumatic duct.
A muscularis mucosa that is part of a fundus of urinary bladder.
muscularis mucosa of fundus of urinary bladder
A muscularis mucosa that is part of a fundus of stomach.
A anatomical space that is enclosed by a fundus of stomach.
A dense fibrous ring surrounding the umbilicus at birth. At about the sixth week of embryological development, the midgut herniates through the umbilical ring; four weeks later it returns to the abdominal cavity and rotates around the superior mesenteric artery.
An elevation on the wall of the embryonic urogenital sinus where the Müllerian ducts enter.
Cavity of ventricle which is surroounded by the wall of right vetricle and is contiuous with the lumen of the pulmonary trunk.
A epithelium that is part of a male urethra.
A lamina propria that is part of a mucosa of fundus of stomach.
lamina propria mucosae of fundus of stomach
A anatomical space that is part of a duodenum.
Cavity of atrium which is surrounded by the wall of left atrium and is continuous with the lumen of the pulmonary vein.
Cavity of ventricle which is surrounded by the wall of left ventricle and is continuous with the lumen of the aorta.
A muscular coat that is part of a prostatic urethra.
muscle layer of prostatic part of urethra
A lamina propria that is part of a prostatic urethra.
lamina propria of prostatic part of urethra
A anatomical space that is part of a jejunum.
A muscularis mucosa that is part of a jejunum.
A epithelium that is part of a female urethra.
Cavity of atrium which is surrounded by the wall of right atrium and is continuous with the lumen of superior vena cava and inferior vena cava.
A muscular coat that is part of a spongiose part of urethra.
muscle layer of spongiose part of urethra
Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border.
Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though
Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified].
We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts.
A cerebral hemisphere white matter that is part of a lobe of cerebral hemisphere.
A white matter of cerebral lobe that is part of a frontal lobe.
A cerebral hemisphere grey matter that is part of a lobe of cerebral hemisphere.
A cerebral hemisphere grey matter that is part of a parietal lobe.
A white matter of cerebral lobe that is part of a parietal lobe.
A white matter of cerebral lobe that is part of a temporal lobe.
A white matter of cerebral lobe that is part of a occipital lobe.
A white matter of cerebral lobe that is part of a limbic lobe.
A cerebral hemisphere grey matter that is part of a temporal lobe.
A cerebral hemisphere grey matter that is part of a occipital lobe.
A cerebral hemisphere grey matter that is part of a limbic lobe.
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
central nervous system gray matter layer
A layer of of the central nervous system that is composed of white matter.
central nervous system white matter layer
subdivision of spinal cord ventral column
mucus produced in the respiratory tract.
Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm).
A white matter that is part of the midbrain.
A stria of neuraxis that is part of a telencephalon.
A blood vessel that is part of a cerebellum.
An roughly circular indentation in a surface.
An acellular membrane in the vestibular labyrinth that is composed of the otoconial layer, gelatinous layer, and a subcupular meshwork.
gelatinous layer of statoconial membrane
An acellular membrane in the inner ear that is part of the statoconial membrane and consists of long branching filaments cross-bridged to one another. The filaments are continuous with those of the otolithic membrane on one side and with the surface of the epithelium on the other.
subcupular meshwork of statoconial membrane
obsolete lamina II of gray matter of spinal cord
lamina III of gray matter of spinal cord
lamina VII of gray matter of spinal cord
lamina VIII of gray matter of spinal cord
Rexed lamina system typically extends to X
The Nucleus proprius is a layer of the spinal cord adjacent to the substantia gelatinosa. Nucleus proprius constitutes the bulk of the dorsal horn and receives inputs from the dorsal root ganglions that carry sensory information, such as light touch, as well as pain and temperature information. Cells in this nucleus project to deeper laminae of the spinal cord, to the posterior column nuclei, and to other supraspinal relay centers including the midbrain, thalamus, and hypothalamus. Rexed laminae III, IV, and V make up the nucleus propius Nucleus proprius (NP), along with nucleus dorsalis (ND) are involved in sensing fine touch and proprioception.
A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix.
auditory hillocks, pharyngeal arch 1 derived
A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus.
auditory hillocks, pharyngeal arch 2 derived
A Y-shaped fibrocartilage structure that lies in the substance of the muscular ventral pouch of rorqual whales.
Y-shaped fibrocartilage skeleton of ventral pouch
A fibrous capsule located between the jaws of rorqual whales that contains a gelatinous substance and papillae bearing mechanorecaptors.
A vibrissa on the lower jaw of rorqual whales that is hypothesized to form part of the lung feeding system.
stem of Y-shaped fibrocartilage skeleton of ventral pouch
branch of Y-shaped fibrocartilage skeleton of ventral pouch
A body structure consisting of nerves traveling together with arteries, veins, and/or lymphatics.
Fibrous joint connecting the actinopterygian frontal bone to the actinopterygian parietal bone.
The parvocellular reticular nucleus is part of the brain located dorsolateral to the nucleus reticularis pontis caudalis. The dorsal portion of the reticular nucleus has been shown to innervate the mesencephalic trigeminal nucleus and its surrounding area. Also, it projects to the facial nucleus, hypoglossal nucleus and parabrachial nucleus along with parts of the caudal parvocellular reticular formation. This nucleus is also involved in expiration with a part of the gigantocellular nucleus.
The premotor cortex is an area of motor cortex lying within the frontal lobe of the brain. It extends 3 mm anterior to the primary motor cortex, near the Sylvian fissure, before narrowing to approximately 1 mm near the medial longitudinal fissure, which serves as the posterior border for the prefrontal cortex. The premotor cortex is largely equivalent to Brodmann area 6. Activity within this region is critical to the sensory guidance of movement and control of proximal and trunk muscles of the body.
The supplementary motor area (SMA) is a part of the sensorimotor cerebral cortex (perirolandic, i.e. on each side of the Rolando or central sulcus). It was included, on purely cytoarchitectonic arguments, in area 6 of Brodmann and the Vogts. It is located on the medial face of the hemisphere, just in front of primary motor cortex. This is an element that appeared late in evolution, in monkeys, linked to the appearance of a true medial pallidum.
Lateral component of the periolivary nucleus
The term subparafascicular nucleus refers to a cell group located ventral to the parafascicular nucleus in the thalamus. Identified by internal structure, it is present in the human ( Mai-1997 ), the macaque ( Paxinos-2009a ), the rat ( Swanson-1998 ), and the mouse ( Hof-2000 ).
subparafascicular nucleus of the thalamus
lateral paragigantocellular reticular nucleus
paragigantocellular nucleus, lateral part
paragigantocellular reticular nucleus, lateral part
dorsal paragigantocellular reticular nucleus
paragigantocellular nucleus, dorsal part
posterior paragigantocellular reticular nucleus
paragigantocellular reticular nucleus, dorsal part
paramedian group (medullary reticular formation)
Small nucleus in the brainstem of human, located adjacent and medial to the nucleus prepositus in the dorsal medulla, described in several atlases of human brain stem. In transverse sections, it is oval with its long axis aligned with the dorsal border of the brainstem. It begins at about the same A-P level as the nucleus prepositus, just rostral to the hypoglossal nucleus. It includes calretinin immunoreactive large cells with oval or polygonal cell bodies. Cells are not immunoreactive for either calbindin or parvalbumin, but a few fibers immunoreactive to each protein are found within its central region. Cells in PMD are also immunoreactive to nNOS, and immunoreactivity to a neurofilament protein shows many labeled cells and fibers. According to Baizer et al., no equivalent structure was observed in the cat, rat, mouse or monkey atlas although they did not look at the brains of the great apes.
nucleus reticularis paramedianus myelencephali
The term paratrigeminal nucleus refers to a group of cells located lateral to the spinal trigeminal tract of the medulla and medial to the spinocerebellar tracts at the level of the spinal trigeminal nucleus. The cells, identified by Nissl stain, are partially embedded in the adjacent tracts; their distribution varies by species. The paratrigeminal nucleus may represent an extension of the lateral cervical nucleus into the medulla ( Swanson-2004 ). It is found in the human ( Carpenter-1983 ), the macaque ( Paxinos-2009a ), the rat ( Swanson-2004 ) and the mouse ( Paxinos-2001 ). In the functional model of central nervous system organization it is classified as part of the subcortical somatosensory system ( Swanson-2004 )
lateral cervical nucleus, trigeminal extension
The term lateral trapezoid nucleus refers to one of two potential parts of the trapezoid nucleus. Separated by an indistinct boundary, the other is the medial trapezoid nucleus ( Crosby-1962 ). The existence of the trapezoid nucleus in the human is disputed ( Bazwinsky-2003 )
The term retroambiguus nucleus refers to a group of neurons in the medulla at the caudal end of the nucleus ambiguus, from which the cranial part of the accessory nerve originates ( Crosby-1962 ).
A cell group located ventral to the brachium conjunctivum in the general area where the medial and lateral parabrachial nuclei abut, shifting to the slightly more lateral position rostrally.
neuron cell bodies located in the more medial portions of the anterior horn at cervical levels C3-C7 that innervate the diaphragm via the phrenic nerve.
nucleus phrenicus columnae anterioris medullae spinalis
phrenic nucleus of anterior column of spinal cord
A fascial pouch derived from extraperitoneal connective tissue that contains the kidneys, the suprarenal glands, the renal vessels and perirenal fat
A skin gland found in the interdigital region of some mammals
The dorsal region of the optic cup that gives rise to the dorsal part of the retina.
The ventral region of the optic cup that gives rise to the ventral part of the retina.
A digit that is part of a digit 6 plus metapodial segment.
A digit that is part of a digit 7 plus metapodial segment.
A digit that is part of a digit 8 plus metapodial segment.
A subdivision of the autopod consisting of digit 6 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.
digit 6 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 7 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 7 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 8 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 8 ( phalanges plus metapodial) plus soft tissue
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 6 plus the associated metapodial element.
this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 7 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 8 plus the associated metapodial element.
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
The craniopharyngeal canal, is an anatomical feature sometimes found in the sphenoid bone opening to the sella turcica. It is a canal (a passage or channel) sometimes found extending from the anterior part of the fossa hypophyseos of the sphenoid bone to the under surface of the skull, and marks the original position of Rathke's pouch; while at the junction of the septum of the nose with the palate traces of the stomodeal end are occasionally present.
An ankle joint that passes between the astragalus and calcaneum.
The ankle joint of pseudosuchians (including crocodilians) and phytosaurs, passing between the astragalus and calcaneum, is also called crurotarsal joint in the literature.[5][6] In the skeletons of the phytosaurs and most of the pseudosuchians this joint bends around a peg on the astragalus which fits into a socket in the calcaneum (the “crocodile normal” tarsus); only in the skeletons of the ornithosuchid pseudosuchians a peg on the calcaneum fits into a socket in the astragalus (the “crocodile reversed” tarsus).[3] Strictly speaking this ankle isn’t a crurotarsal joint in the previously discussed sense, as it's situated between the two proximal tarsal bones. However, while calcaneum isn’t fixed to the fibula, the astragalus is fixed to the tibia by a suture and thus in practice it functions as an extension of the crus.[7]
A shallow depression on the lateral wall of the pelvis. This fossa has the following boundaries: superiorly: by the external iliac vessels anteriorly and inferiorly: by the broad ligament of the uterus posteriorly: by the ureter and internal iliac vessels
The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints
Epithelium lining the distalmost portion of the digestive tract.
epithelium of terminal part of digestive tract
Any muscle structure of the distalmost portion of the digestive tract.
muscle of terminal part of digestive tract
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A periosteum that is part of a long bone.
A frenulum of lip that is part of a upper lip.
A frenulum of lip that is part of a lower lip.
electron-lucent layer of basal lamina of connective tissue
A vermilion that is part of a upper lip.
A vermilion that is part of a lower lip.
Area of aorta proximal to the ductus arteriosus.
Area of aorta distal to the ductus arteriosus.
Area of aorta at the area of insertion to the ductus arteriosus.
A coating of mucus that is produced by the skin and covers all or most of the body of an animal.
The epidermal mucus of fish regulates swimming speed by controlling the hydrodynamic resistance of the skin surface. The mucus is also presumed to serve as a defence against pathogenic organisms and is intimately associated with osmoregulation.
A mucous covering produced nocturnally by some fish that is used to envelope the whole animal.
A medially (towards the tongue)) raised feature found on crown of a tooth.
Triangular ridges facing each other and crossing at transverse angle, forming a transverse ridge on posterior teeth.
M. flexor cruris lateralis pars accessoria
pars accessoria of M. flexor cruris lateralis
flexor cruris lateralis pars accessoria muscle
A synovial joint that connects a vertebral bone 1 and connects a exoccipital bone.
A anatomical space that is enclosed by a hemipenal sheath.
A gland within the hemipenial sheath that provides lubrication for the hemipenis.
A holocrine gland that is part of a hemipenis.
A bony structure embedded in skin, roughly equivalent to osteoderms.
Cloacal gland in female salamanders that secrete into the dorsal walls of the cloaca, anterior and / or posterior to the spermathecae or near the spermathecal common tube
A keratinized stratified squamous epithelium that is part of a hemipenis.
A small protuberence on the lingual surface of the premaxilla, immediately posterior to the teeth.
An anatomical group consisting of a placental caruncle and a placental cotyldeon, a placental unit in some mammals such as ruminants.
A sesamoid element that is part of a tarsal skeleton.
The portion of the teeth, occurring on the lingual or palatal aspects, that forms a convex protuberance at the cervical third of the anatomic crown. It represents the lingual or palatal developmental lobe of these teeth.
FMA has no definition but places this generically with upper, lower, canine, incisor subclasses. Wiktionary states cingulum is lower jaw molar only, and cingulid is upper molar only
A ridge that girdles the base of a lower molar tooth
A set of teeth in which each tooth that attaches to a vomer.
A section of a pharyngeal arch artery that carries blood away from the spiracle.
A section of a pharyngeal arch artery that drains the spiracle.
The Extensor pollicis brevis lies on the medial side of, and is closely connected with, the Abductor pollicis longus.
A spine appendage that is part of a head.
One of the spines, probably denticle derivatives, occurring singly or in pairs just behind the orbit on the cheek area in some fossil sharks. May have occurred only in males and may have served to hold the female during copulation, e.g. in the Jurassic genera Hybodus, Asteracanthus and Acrodus.
A supplemental clasper in Holocephali, in front of the pelvic fin
one or more pairs of stiff ossified lobes or prongs found in the tip of the intromittent organ of Bythitoidei
A gland of uncertain function at the base of the clasper in skates and rays, occupying the position of the siphon of other Elasmobranchii.
Houston's valves (or transverse folds of rectum) are semi-lunar transverse folds of the rectal wall that protrude into the anal canal. Their use seems to be to support the weight of fecal matter, and prevent its urging toward the anus, which would produce a strong urge to defecate. Although the term rectum means straight, these transverse folds overlap each other during the empty state of the intestine to such an extent that, as Houston remarked, they require considerable maneuvering to conduct an instrument along the canal, as often occurs in sigmoidoscopy and colonoscopy. These folds are about 12 mm. in width and are composed of the circular muscle coat of the rectum. They are usually three in number; sometimes a fourth is found, and occasionally only two are present. One is situated near the commencement of the rectum, on the right side. A second extends inward from the left side of the tube, opposite the middle of the sacrum. A third, the largest and most constant, projects backward from the forepart of the rectum, opposite the fundus of the urinary bladder. When a fourth is present, it is situated nearly 2.5 cm above the anus on the left and posterior wall of the tube.
A thin diaphragm located in the posterior fifth of the intestine of some Centrolophidae, e.g. Seriolella punctata, Schedophilus huttoni and Psenes pellucidus, or in others a sphincter-like constriction, e.g. Seriolella brama. A deep purple fluid was confined to the valve in S. punctata, but was found throughout the intestine in the other two species referred to. The fluid might be used to void a coloured cloud to distract or deter a predator.
A structure with numerous blood vessels (retia mirabilia) in the gas bladder that secretes gases from the blood.
An innervated group of cells in a round capsule at the end of a jelly-filled tube opening to the skin surface of Gymnarchidae and Mormyridae.
A calcified structure of brain that is part of a pineal body.
A calcified structure of brain that is part of a choroid plexus.
A supplementary intervertebral articulation found in xenarthrans characterized by two sets of zygapophyseal facets in the postdiaphragmatic vertebrae, one medial and one lateral to the met apophysis
A paired dural venous sinus at the rim of the foramen magnum.
The primitive marginal sinuses (PMS) are embryonic sinuses forming the later superior sagittal sinus.
A circular gap in the iris near the pupil between the layers of the optic cup (von Szily, 1902)
Branch of spinal nerve that innervates the structures of the vertebral column.
recurrent meningeal branch of spinal nerve
extension of the long thoracic vein that collects blood from the mammary glands
One of two veins running parallel to their corresponding internal mammary arteries that unite forming one vessel. These veins drain the chest wall into the innominate vein.
A prevertebral muscle that is part of a neck.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
A primordium that has_potential_to_develop_into a saliva-secreting gland.
A gland lodged in a fossa formed mainly of dermal bones, situated wholly in front of the nasal capsules of Osteolepiformes.
intermaxillary gland (sensu Osteolepiformes)
A gland located at the pre-nasal area being divided anteriorly by the ascendent processes of the intermaxillary bone.
The intermaxillary gland is the first salivary gland to appear in the vertebrate evolution. Its duct system is uniformly lined by ciliated cells and scattered secretory cells. This indicates that in the evolution, of salivary glands, there was a diversification of the duct system, together with progressxve concentration of secretory cells in special áreas of this system
Although usually described in the literature as mucous, the secretory cells of the intermaxillary gland have serous characteristics.
Any of the small racemose mucous glands in the mucous membrane lining the cheeks
A bony part of vertebral arch that is part of a cervical vertebral arch.
A bony part of vertebral arch that is part of a sacral vertebra 1.
bony part of vertebral arch of first sacral segment
bony part of vertebral arch of first sacral vertebra
internal (endosteal) surface of the base of skull
A primary incisor tooth that is part of a lower jaw region.
he ridge between the shoulder blades of a four-legged mammal.
The withers in horses are formed by the dorsal spinal processes of roughly the 3rd through 11th thoracic vertebrae (most horses have 18 thoracic vertebrae), which are unusually long in this area. The processes at the withers can be more than 12 inches (30 cm) long.
A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton.
awaiting approval by phenoscape curators
proximal mesopodial endochondral element
A proximal mesopodial endochondral element that is composed primarily of a cartilage tissue.
An endochondral element in the distal portion of the mesopodial skeleton, between the central mesopodial skeleton and the metapodial skeleton
A distal mesopodial endochondral element that is composed primarily of a cartilage tissue.
A distal mesopodial endochondral element that is composed primarily of a pre-cartilage condensation.
distal mesopodial pre-cartilage condensation
A distal mesopodial endochondral element that is composed primarily of a bone tissue.
The thinner portion of the muscle of the palatopharyngeal arch, originating in the region of the midline where its fibers interdigitate with the contralateral partner, then passing posterior to the levator veli palatini muscle to join the longitudinal layer of pharyngeal musculature; acts as a sort of sphincter, reducing the caliber of the isthmus of fauces at the palatopharyngeal arch.
fasciculus posterior (musculus palatopharyngeus)
The intermediate belt surrounding the fovea centralis
ganglion cell layer is composed of more than five rows of cells, as well as the highest density of cones
The outermost region surrounding the fovea centralis
the ganglion cell layer contains two to four rows of cells
A region of the fovea centralis that lies in the center of the fovea and contains only cone cells, and a cone-shaped zone of Müller cells
in humans is approximately 0.35 mm in diameter
The superior auricular muscle, the largest of the three auriculares muscles, is also thin and fan-shaped. Its fibers arise from the galea aponeurotica, and converge to be inserted by a thin, flattened tendon into the upper part of the cranial surface of the auricula.
The anterior auricular muscle, the smallest of the three auriculares muscles, is thin and fan-shaped, and its fibers are pale and indistinct. It arises from the lateral edge of the galea aponeurotica, and its fibers converge to be inserted into a projection on the front of the helix.
The posterior auricular muscle consists of two or three fleshy fasciculi, which arise from the mastoid portion of the temporal bone by short aponeurotic fibers. They are inserted into the lower part of the cranial surface of the concha.
A muscle layer that is part of the rectum
Any portion of smooth muscle tissue that is part of the rectum
A kidney interstitium that is part of a right kidney.
A kidney interstitium that is part of a left kidney.
A renal pelvis that is part of a left ureter.
A renal pelvis that is part of a right ureter.
A renal cortex interstitium that is part of a left kidney.
cortical interstitial tissue of left kidney
A renal cortex interstitium that is part of a right kidney.
cortical interstitial tissue of right kidney
A renal medulla interstitium that is part of a left kidney.
medullary interstitial tissue of left kidney
A renal medulla interstitium that is part of a right kidney.
medullary interstitial tissue of right kidney
The encapsulated adipose tissue associated with the ovaries.
Encapsulated adipose tissue that is part of a tail.
The platypus uses its tail for storage of fat reserves (an adaptation also found in animals such as the Tasmanian devil and fat-tailed sheep)
A folded ridge of skin that is part of a scrotum superficial to the dartos muscle
A fenestra or hole which pierces the maxilla anterior to the antorbital fenestra.
A fenestra that is part of a premaxilla.
A cluster of mammary gland lobules. In humans this is a distinct lobe and located in the breast region.
The FMA class 'lactiferous gland' may be equivalent to this
Regional part of telencephalon lying on the basal surface and bounded by the olfactory trigone rostrally, the diagonal band medially and caudally and the prepiriform cortex laterally. It is characterized by many perforations caused by small blood vessels entering the gray matter (Meyer et al., J. Comp. Neurol 284: 405, 1989).
Subdivision of telencephalon which is a region on the ventro-medial aspect of the telencephalon penetrated by numerous blood vessels. It is bounded by the optic tract posteriorly and the olfactory trigone anteriorly.
Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx).
A transverse process that is part of a cervical vertebra
May be homologous with the cervical ribs of some vertebrates
A rib that is attached to a cervical vertebra.
May be homologous with the transverse processes of cervical vertebra
Trunk, presacral and sacral ribs do not have a "part of some region" asserted for them, we should add it to them[PHENOSCAPE:ad]
A rib that is attached to a lumbar vertebra.
May be homologous with the transverse processes of lumbar vertebra
A transverse process that is part of a lumbar vertebra
May be homologous with the lumbar ribs of some vertebrates
A bodily secretion that produced_by a ampullary gland.
A zone of skin that is part of a lower lip.
A zone of skin that is part of a upper lip.
A small, triangular, flaccid portion of the tympanic membrane, or eardrum, lying above the malleolar folds, attached directly to the petrous bone at the notch of Rivinus.
Size varies across mammals, with the sheep pars flaccida larger than the human
A ligament that is part of a middle ear.
A fold of mucous membrane that runs from the fossa incudus to the incus.
A skeletal ligament that attaches to the malleus.
A malleal ligament that extends from the bony margin of the notch of Rivinus to the neck of the malleus.
A malleal ligament that extends from the tempen tympani to the head of the malleus.
A malleal ligament that extends from the anterior tympanic wall to the anterior process of the malleus.
A ring of fibrous tissue that connects the base of the stapes to the oval window of the inner ear.
A anatomical cluster that is part of a lung and is part of a lymphatic part of lymphoid system.
A lymphatic vessel that is part of a lung.
A system consisting of renin, angiotensin-converting enzyme, and angiotensin II. Renin, an enzyme produced in the kidney, acts on angiotensinogen, an alpha-2 globulin produced by the liver, forming angiotensin I. The converting enzyme contained in the lung acts on angiotensin I in the plasma converting it to angiotensin II, the most powerful directly pressor substance known. It causes contraction of the arteriolar smooth muscle and has other indirect actions mediated through the adrenal cortex.
may be replaced by a GO process in future
The compartment of the femoral sheath that contains efferent lymphatic vessels and a lymph node embedded in a small amount of areolar tissue. It is conical in shape and is about 2 cm long. The femoral canal is bordered: Anteriorly by the inguinal ligament Posteriorly by the pectineal ligament Medially by the lacunar ligament Laterally by the femoral vein It contains the lymph nodes of Cloquet or Rosenmuller. It should not be confused with the nearby adductor canal.
A long slender branch of the anterior inferior cerebellar artery (85%-100% cases) or basilar artery (<15% cases), arises from near the middle of the artery; it accompanies the vestibulocochlear nerve through the internal acoustic meatus, and is distributed to the internal ear.
Glands of Zeis are unilobar sebaceous glands located on the margin of the eyelid. The glands of Zeis service the eyelash. These glands produce an oily substance that is issued through the excretory ducts of the sebaceous lobule into the middle portion of the hair follicle.
A capsule that divides the parenchyma of the pancreas into lobes and lobules
A midline nucleus of the dorsal motor column found in animals with a prominent tail, including alligator, some birds, kangaroo, rat, shrew, great anteater.
A sensory tract originating in the spinal cord responsible for transmitting fine touch, vibration and conscious proprioceptive information from the body to the cerebral cortex. The components include the fasciculus gracilis and fasciculus cuneatus.
posterior column-medial leminscus pathway
posterior column-medial lemniscus system
posterior column/medial leminscus pathway
A nucleus that contain secondary neurons of the dorsal column-medial lemniscus pathway, which carries fine touch and proprioceptive information from the body to the brain. Examples: gracile nucleus, cuneat nucleus, nucleus of Bishoff.
The skeletal muscle layer in the superficial fascia deep to the panniculus adiposus
In humans, the platysma has features of the panniculaus carnosus[ISBN10:0123813611].
fine, flat muscles within the hypodermis. Their origin is in the deep fascia of bone and they insert into superficial skin. Function notes: They act to raise hair, quills, feathers, etc. It is also used in 'twitch' reflexes to shake off insects, etc.[Palaeos]
A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence.
The part of the palatine bone that forms the posterior part (approximately one third) of the bony palate.(Stedmans)
A vein that supplies blood to the thymus.
thymic branch of internal thoracic artery
The arteries supplying the thymus are derived from the internal thoracic artery, and from the superior thyroid artery and inferior thyroids.[WP]
A cervical thymus that is located directly beneath the skin.
apparently absent in polyprotodont species (Didelphidae, Dasyuridae, Thylacinidae, Notoryctidae, Peramelidae, and Caenolestidae); paired lobes found in diprotodont (Burramyidae, Petauridae, Phalangeridae, Phascolarctidae, and Tarsipedidae)[doi:10.1071/ZO9730285]
A cervical thymus that is located deep in the ventral cervical region, superficial to hyoid, sternomastoid, and depressor neck muscles.
A artery that supplies a cervical thymus.
inferior superficial cervical thymic artery
superior superficial cervical thymic artery
In Cavio cobaya, arises from the external carotid or distal half of the common carotid artery, passed the thyroid gland cranially or penetrated it to terminate in the inferior laryngeal artery
In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault.
Accompanying vein of internal pudendal artery.
In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins
One of the veins of the pelvis which drain into the great saphenous vein.
Added for consistency with MA EMAPA and EHDAA2. See https://sourceforge.net/p/obo/mouse-anatomy-requests/90/
jejunal branch of superior mesenteric artery
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
A muscular coat that is part of a digestive tract.
responsible for gut movement, such as peristalsis
entorhinal area, medial part, dorsal zone
dorsal zone of the medial part of the entorhinal area
entorhinal area, medial part, dorsal zone, layers 1-6
entorhinal area, medial part, ventral zone
entorhinal area, medial part, ventral zone [Haug]
ventral zone of the medial part of the entorhinal area
ventral zone of medial entorhinal cortex
The dorsal region of the lateral ganglionic eminence. The cells in this area give rise to embryonic interneuron precursors that will migrate tangentially to the olfactory bulb.
The anterior or rostral end of the zygomatic arch, which includes the temporal process of the zygomatic bone, but also including some of the body of the zygomatic bone. It may also include the zygomatico-temporal suture and the most rostral portion of the zygomatic process of the temporal bone.
requires definition see https://github.com/obophenotype/uberon/issues/492
The third phalangeal bone in a digit ray.
to be discussed. Should this class be used for the distal phalanges on a 3-phalanx ray (e.g. human finger 2?)
Foramen housing the root of the spinal nerve seen in the neural arch of the first vertebrae (atlas). (see Edwards 1976)
In extant taxa this is restricted to some members of Caudata
Adrenal tissue dispersed in clusters, found in periphery and center of adranal gland in turtles (Yadav, 2008).
Adrenal tissue aggregated in a dorsal layer covering internal cords, found in lepidosaur adrenal glands. Islets of adrenal tissue found on ventral surface of gland (barely present in squamates). See Yadav, 2008.
Adrenal tissue found in archosaurs - tissue arranged in bands, alternating with interrenal cords (Yadav, 2008)
In mammals, adrenal tissue has a cortex and medulla creating a composite adrenal gland (Kardong 2012)
The highest elevation of the paracone on a molariform tooth.
The anterior region of the maxillary tooth row, if that tooth row contains teeth that are substantially over the premaxillary teeth (see Laurin and Reisz 1995)
A postcingulum found on deciduous premolar 5
A posthypocrista found on deciduous premolar 5
A protuberence or true tooth that is used during hatching to break the eggshell.
Tooth used to break the eggshell, that is shed soon after hatching. In lepidosaurs, a true tooth that is shed soon after hatching.
in lepidosaurs, a true tooth that is shed soon after hatching
Epidermal outgrowth that facilitates breaking of the eggshell in archosaurs and monotremes.
The labial most of three cusps on the talonoid (posterior) end of lower molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
Fifth premolar (counting anteroposteriorly ) in the lower jaw.
Third molar (counting anteroposteriorly) in the lower jaw.
Pharyngeal toothplate of the lower jaw region; typically associated with ceratobranchial 5 element.
need to add relationship: UBERON:'pharyngeal tooth plate' needs relationship part_of 'splanchnocranium'
First premolar (counting anteroposteriorly ) in the lower jaw.
Second premolar (counting anteroposteriorly ) in the lower jaw.
Posteroloph found on the first molar tooth.
Hypoconid found on the first premolar tooth.
The anterior cusp along the labial margin seen in the molar or premolar teeth of mammals. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
A crest running along the labial margin of molarifomr teeth of mammals. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
A shelf like ridge on the posterior (distal) outside edge of the upper molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
A shelf like ridge on the outside of the upper molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
A crest on the hypoconid of molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
A shelf like ridge on the proximal (mesial) outside edge of the upper molariform teeth. (modified from http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure/)
First premolar (counting anteroposteriorly) in the jaw.
An enamel ridge joining the protocone and the paracone on the occlusal surface of a maxillary molar.
Tooth (often obscured from view) in a 'waiting' position that will replace an existing tooth (i.e. a tooth that is well visible in the jaw)
additional feedback required. Should this be classified as a primary tooth?
A pit formed in an existing functional tooth, causing resorption of the surrounding dentine and periodontal tissues. (modified from LeBlanc and Reisz 2013, see figures 8, 10 for more details)
Cusp found on a platform that is buccaal and mesial to the meta and paracones. Modified from Kermack 1967. Molar evolution in Mesozoic mammals
Tooth of the lower jaw that is adjacent to the mandibular symphysis
first canine (counting anteroposteriorly) in the upper jaw.
Fifth premolar (counting anteroposteriorly ) in the upper jaw.
first molar (counting anteroposteriorly) in the upper jaw.
Tissue that is part of some adrenal gland
TODO - describe typology of adrenal gland tissue used in this ontology
Anatomical region lying to the posteiror or ventral side of the metapterygial axis.
region of the humerus associated with the biceps attachment areas
expanded and swollen region of a surface that is otherwise relatively flat
Ridge shaped projection, similar to the keel of a boat
distinct colored area on the caudal region of an organism, similar in shapre to a spot, i.e. circular.
Anatomical structure consisting of a pattern of ridges on an osteoderm.
A dermal scale that is found in the head region
A row of scales foudn in the cheek region of the head of an organism.
grooves on the palatine bone which denote the passage of the choana or internal naris
Pelvic clasper organs that have been modified into a flattened structure
currently created as a subtype of clasper, but it's not clear when modifications are sufficient to create a new class[cjm]
Facet on the anterior surface of the calcaneus (as called calcaneum) for the articulation of the cuboid bone
Osteoderm found on the dorsal surface of an organisms.
A depression on the lateral surface of the braincase posterior to the Vidian canal (Conrad 2008)
Section of the oviduct external to the uterine wall.
A sesamoid bone located near or in the flexor musculature of a joint.
Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX).
fourth most proximal phalanx in manual or pedal digits.
Area on the otic capsule for the articulation of the hyoid
Caudal fin radial element located ventral to the notochord
Radial element that is part of the caudal fin.
Situated just caudal to the acetabulum, the foramen is bound dorsally by the illium and ventrally by the ischium. The foramen transmitts the ischiadic nerves and vessels (Baumel et al. 1993)
The condyloid fossa on the cranial aspect of the Atlas my be perforated (foramen fossa) or have an open dorsal notch (Incisura fossa) in which the apex of the dens rides. (From Baumel et al. 1993)
The region on the palate corresponding to the location of the pterygoid bone, if present and between the palatine bones and the parasphenoid if not.
propose changing palate bone to palate bone series[PHENOSCAPE:ad]
Open space between on the palate between the pteryogoid bone and the parasphenoid
A joint in the lower jaw that enhances kinesis and for swallowing prey. Allows enhanced mobility and intraramal bending to increase gape.
elongate bar consisting of fused quadratojugal and jugal and connecting the maxilla to the quadrate
Distinct cartilage around the jaws of elasmobranchs
Condyle on the lateral side of the quadrate
One of the branches of the dorsal aorta, after it enters the aortic canal
The triangular shaped posterior fold at the angle of the mouth. From Chakrabarty 2006
The medialmost condyle on the distal region of the quadrate, in contact with the pterygoid.
The medialmost of the cotyla of the lower jaw, for articulation with the cranium.
According to Uberon mandible only denotes the dentary of mammals. THis is incorrect[PHENOSCAPE:ad]
An embryonic fissure between the otic capsule and the arches which develop into the occipital bones. The fissure may persist into adulthood. It is also referred to as the 'lateral otic fissure' The metotic fissure opens into the vestibular fontanelle, if the fontanelle is present. (Johanson et al. (2003)). Otherwise it opens to the metotic foramen.
distinct colored area on the midbody region of an organism, similar in shapre to a spot, i.e. circular.
A bony projection of the premaxilla that extends cadually and separates the nasal bones.
Dorsal swelling on the head. Found in cichlid fish. Often only in males and during breeding season, but not exclusively so.
The wall of the fallopian tube includes an elaborately folded mucosa (endosalpinx) surrounded by a muscularis (myosalpinx). The mucosa is lined by a ciliated columnar epithelium with secretory cells, and is folded out into the lumen so that an ovum in the lumen will always be close to the cilia for transport to the uterus.
An anterior cusp on the stylar shelf of the tooth
The stylar shelf is an an expansion of the cingulum; it often bears small cusps (each with its own name...).
A pronounced notch or cavity in the lateral face of the parietal.
distinct from UBERON:0001694 petrous part of temporal bone; [http://www.ncbi.nlm.nih.gov/pubmed/19438763]
Ventral process on the neurocranium for the articulation of upper pharyngeal bones. It is variably composed of the parasphenoid, basioccipital, and prootic depending on the species. From: Greenwood, PH (1978). A review of the pharyngeal hypophysis and its signiﬁcance in the classiﬁcation of African cichlid ﬁshes. Bull. Br. Mus. Nat. Hist. (Zool.) 33: 297-323.
The lack of chondrification of the anterior wall of the cranial cavity in front of the pineal foramen.....(Hanken and Hall)
cartilage arranged into tesserae, blocks of calcified cartilage that fit together as tiles on a floor form a mosaic. Found only in chondrichthyans. Reference: A. Peter Klimley. 2013. The Biology of Sharks and Rays. University of Chicago Press.
The convex articular surface on the qudrate, part of the craniomandibular joint.
As defined here, this refers to a depression on the lateral surface of the braincase posterior to the Vidian canal as opposed to the carotid fossa...(Conrad 2008)
Rictal bristles project from the beak of many insect-eating birds, including flycatchers, nightjars and even the American Robin. They are believed to provide protection for the bird's eyes as it consumes its wriggly prey. The bristles may also provide tactile feedback, like the whiskers on a dog or cat. from http://www.birds.cornell.edu/AllAboutBirds/studying/feathers/feathers/document_view
An entotympanic that arises in forward part of tympanic floor. It may be intimately fused witA cartilage of tube during development(MacPhee (1981: 62)) in contrast to a caudal entotympanic arising in the rear tympanic floor. From O'Leary et al. 2012
A median bony point projecting from the anterior and ventral margin of the sternum of a bird. From http://www.merriam-webster.com/dictionary/spina%20externa
The ventral portion of the frontals which forms part of the lateral wall of the braincase. Modified from Lee and Caldwell 1998
Foramen located below the orbit and forming a passageway for nerves (eg fifth cranial nerve)
On the neurocranium, a horizontal plate arising on the ventral junction of the orbital wall and basal plate on each side which extends from the nasal capsule to the otic capsule; it forms the floor of the orbit. A well-developed suborbital shelf is apparently primitive for shark-like fishes but is variably telescoped, reduced or lost in many squalomorph sharks and a few galeomorphs.
Definition from: LJV Compagno. 2002. Sharks of the World Volume 2; FAO Species Catalogue for Fishery Purposes No. 1
Anatomical projection on the distal region of the femur or humerus and close to the condyles.
Opening for the supracoracoid nerve in the supracoracoid.
Foramen in the temporal bone, adjacent to the base of the zygomatic process.
ossified bridge over a tendon; Particularly, the bridge over the extensor canal at the distal end of the tibiotarsus of certain birds. The presence of the bridge and the position of the canal opening relative to the condyles may have phylogenetic significance. Ericson (1997). http://palaeos.com/vertebrates/glossary/glossarySq.html
The crest is present on the ventral side of the bodies of the thoracic vertebra (modified from Baumel et al. 1993)
hypapophysis, Crista ventralis corporis, Crista ventralis, Processus latus
processus ventralis of thoracic vertebra
Ventrolaerally oriented, paired projections atttached to the ventrolateral border of the body of certain thoracic vertebra; the ventrolateral crest flank the crista ventralis on each side. From Baumel et al. 1993
Crsita ventrolateralis, Processus inferolateralis
processus ventrolateralis of thoracic vertebra
dorsal sensory canal line in fish, dorsal to ventral lateral lane
consider merging with UBERON:0003095 ! dorsal lateral line
ventral sensory canal line in fish, ventral to dorsal lateral lane
tubercle on the distal humerus for the origin of the Lig. collaterale ventral of the elbow joint. Modified from Baumel et al. 1993
tubercle on the dorsal border of the distal humerus, a short distance from the dorsal epicondyle, for the origin of the m extensor carpe radialis modifeid from Baumel et al. 1993
A unit of the tectoral membrane that is shaped like string of flat, pearls. Modified from Manley, Fey and Popper 2008; see also http://books.google.com/books?id=oZaaal687X8C&pg=PA227&lpg=PA227&dq=sallet+inner+ear&source=bl&ots=Y7e2_zTIoi&sig=dFLn4yvWwdEV55_uMYkzGMrTGY8&hl=en&sa=X&ei=S_aVU9HvDKWysATtx4G4DA&ved=0CHUQ6AEwDQ#v=onepage&q=sallet&f=false
The larval stage of a crustacean, the stages of which are separated my moults. Typically this goes through a nauplius - zoea - post-larval cycle.
The larval (metacestode) stage of the tapeworm Echinococcus multilocularis.
Instar: a stage in the life of an arthropod (as an insect) between two successive molts.
A tailless encysted late larva of a trematode parasite that is usually the form which is infective for the definitive host.
Any of a class (Cestoda) of bilaterally symmetrical flatworms parasitic especially in the intestines of vertebrates.
A usually tadpole-shaped larval trematode worm that develops in a molluscan host from a redia.
A sensory receptor that detects stimulus within the body. Examples of stimuli that would be detected by interoceptors include blood pressure and blood oxygen level.
A sensory receptor that detects chemical stimulus within the body.
Arterial baroreceptors are stretch receptors that are stimulated by distortion of the arterial wall when pressure changes.
found in large systemic veins, in pulmonary vessels, and in the walls of the right atrium and ventricles of the heart (the atrial volume receptors).
A baroreceptor that located_in a pulmonary vascular system.
The posterior superior alveolar artery (posterior dental artery) is given off from the maxillary, frequently in conjunction with the infraorbital just as the trunk of the vessel is passing into the pterygopalatine fossa.
The posterior superior alveolar branches (posterior superior dental branches) arise from the trunk of the maxillary nerve just before it enters the infraorbital groove; they are generally two in number, but sometimes arise by a single trunk. They descend on the tuberosity of the maxilla and give off several twigs to the gums and neighboring parts of the mucous membrane of the cheek. They then enter the posterior alveolar canals on the infratemporal surface of the maxilla, and, passing from behind forward in the substance of the bone, communicate with the middle superior alveolar nerve, and give off branches to the lining membrane of the maxillary sinus and gingival and dental branches to each molar tooth from a superior dental plexus; these branches enter the apical foramina at the roots of the teeth. The posterior superior alveolar nerve innervates the second and third maxillary molars, and two of the three roots of the maxillary first molar (all but the mesiobuccal root). When giving a Posterior Superior Alveolar nerve block, it will anesthetize the mesialbuccal root of the maxillary first molar approximately 72% of the time.
The infraorbital foramen is located above the second cheek tooth in the maxilla. Immediately rostral to the foramen, the bone is often cribriform, covering a honeycomb area between medial and lateral plates of the maxilla. The infraorbital nerve exits the skull via this foramen.
A branch of the maxillary nerve that enters the infraorbital canal. This nerve innervates the lower eyelid, upper lip, and part of the vestibule and exits the infraorbital foramen of the maxilla.
Near the middle of the posterior part of the orbital surface of the maxilla is the infraorbital groove (or sulcus), for the passage of the infraorbital vessels and nerve. The groove begins at the middle of the posterior border, where it is continuous with that near the upper edge of the infratemporal surface, and, passing forward, ends in a canal, which subdivides into two branches.
a lymphatic capillary that absorbs dietary fats in the villi of the small intestine.
A skeletal ligament that is part of a hip joint.
A nerve that is formed by the junction of the great petrosal nerve and the deep petrosal nerve in the cartilaginous substance which fills the foramen lacerum. It passes forward, through the pterygoid canal, with the corresponding artery, and is joined by a small ascending sphenoidal branch from the otic ganglion. Finally, it enters the pterygopalatine fossa, and joins the posterior angle of the pterygopalatine ganglion. It contains preganglionic parasympathetic fibers from the greater petrosal nerve, a branch of the facial nerve (CN VII), and postganglionic sympathetic fibers from the deep petrosal nerve.
FMA classifies as an anatomical junction
A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen . It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment .
There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)]
Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina
A foramen of skull that is part of a petrosal bone.
A vascular foramen opening on the outer surface of a nasal bone.
A inguinal ring that is part of a female reproductive system.
A inguinal ring that is part of a male reproductive system.
A deep inguinal ring that is part of a female reproductive system.
A deep inguinal ring that is part of a male reproductive system.
the continuation of each corpus cavernosum of the penis or clitoris, diverging posteriorly to be attached to the pubic arch.
Obsoleted as NN retricts this to brainstem structures
obsolete spinal cord reticular formation
A feather that is part of a forelimb wing.
A feather that is part of a the upper ventral region of an animal's torso.
A feather that is part of a the dorsal region of an animal's torso.
A feather tract that is part of a the upper ventral region of an animal's torso.
The region of the mandible on or near the midline (near the mandiblular symphysis)
The anatomical space within the intestine.
see notes in inclusivity in class 'intestine'
Muscle innervated by the trigeminal nerve (Cranial Nerve V).
muscle innervated by the trigeminal nerve
muscles innervated by the trigeminal nerve
The term nucleus of the bulbocavernosus refers to a cluster of motoneurons located in the anterior gray column of lumbar segments 5 and 6 of the spinal cord in the rat. Functionally it belongs to the somatic motoneuron pools of the subcortical motor system ( Swanson-2004 )
Before birth, male and female rats have the muscles and the SNB motoneurons innervating them, but both die in females in the first week of life[https://www.msu.edu/~bjlab/snb.html]
Region where blood progenitor markers are expressed. Probable site of definitive hematopoiesis between 36hpf and 4dpf.
dorsal aorta - posterior cardinal vein joint
A secondary canine tooth that is part of a upper jaw region.
A secondary canine tooth that is part of a lower jaw region.
A lower jaw incisor that is in_the_central_side_of a dentition.
mandibular central secondary incisor tooth
A lower jaw incisor that is in_the_lateral_side_of a dentition.
mandibular lateral secondary incisor tooth
TODO - tooth numbering nomeculature to be aligned across species
maxillary first secondary premolar tooth
maxillary second secondary premolar tooth
mandibular first secondary premolar tooth
mandibular second secondary premolar tooth
A primary incisor tooth that is part of a upper jaw region.
A upper primary canine tooth that is in_the_central_side_of a dentition.
A upper primary canine tooth that is in_the_lateral_side_of a dentition.
A lower primary incisor tooth that is in_the_central_side_of a dentition.
A lower primary incisor tooth that is in_the_lateral_side_of a dentition.
A primary canine tooth that is part of a upper jaw region.
A primary canine tooth that is part of a lower jaw region.
A incisor tooth that is in_the_central_side_of a dentition and is part of a lower jaw region.
A incisor tooth that is in_the_lateral_side_of a dentition and is part of a lower jaw region.
A incisor tooth that is in_the_central_side_of a dentition and is part of a upper jaw region.
A incisor tooth that is in_the_lateral_side_of a dentition and is part of a upper jaw region.
The subdivision of the dentition that consists entire of incisor teeth.
Often called the carnassial tooth, this tooth acts with its counterpart in the lower jaw (the 1st molar in that case) to slice food in a scissoring action.[MURDOCH:2142]
The peristomium is the second body segment in an annelid worm's body in the anterior end. It is directly behind the prostomium and contains the mouth, tentacular cirri, and sometimes feeding palps, which may instead occur on the prostomium. If an eversible pharynx is present, it is contained in this segment as well, and can fill up to 20 segments when inverted, depending on the species.
A triangular hole in the base of the skull located at the base of the medial pterygoid plate.
For comparative reasons this term can only be used for the opening between the Os temporale, Os basisphenoidale, and Os occipitale (formerly the Foramen lacerum orale of the pig and horse). That which was formerly called Foramen lacerum aborale is the Foramen jugulare [NOMINA ANATOMICA VETERINARIA (2005)]
A hollow space in the skull of carnivores, which do not exhibit a maxillary sinus.
consider adding grouping with maxillary sinus
Bounded medially by the Lamina orbitalis of the Os ethmoidale and laterally by the Maxilla and Os palatinum and in the dog also by the Os lacrimale[NOMINA ANATOMICA VETERINARIA (2005)]
The anterior ethmoidal foramen, situated about the middle of the lateral margin of the olfactory groove, transmits the anterior ethmoidal vessels and the anterior ethmoidal nerve; the nerve runs in a groove along the lateral edge of the cribriform plate to the slit-like opening above mentioned.
The posterior ethmoidal foramen opens at the back part of this margin under cover of the projecting lamina of the sphenoid, and transmits the posterior ethmoidal vessels and nerve.
This is present in the cat and forms the large medial part of the Bulla tympanica. It is not to be regarded as a part of the pars tympanica, which ossifies directly from connective tissue, whereas the Pars endotympanica is preformed in cartilage. The Septum bullae in the cat is formed by the Pars tympanica as well as by the Pars endotympanica(NOMINA ANATOMICA VETERINARIA (2005)).
A chitin-based cuticular shell derived from the cuticle of the final larval instar that surrounds the pupal form of the organism
Any acellular shell or covering that surrounds the pupal form of an insect
An opening of the otic duct within the inner ear. The recessus basilaris can open to the saccule (in frogs) or the lagena (in salamanders and caecilians). The sensory epithelium of the recessus basilaris is the basilar papilla (or papilla basilaris). Reference: Lewis, E.R. and R.E. Lombard. 1988. The amphibian inner ear. Pp. 93–123 in Fritszch, B., et al. (eds.), The Evolution of the Amphibian Auditory System. Wiley & Sons. [curated by D. Blackburn]
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
A splanchnic nerves that arises from sacral spinal nerves S2, S3, S4 to provide parasympathetic innervation to the hindgut.
The renal plexus is formed by filaments from the celiac plexus, the aorticorenal ganglion, and the aortic plexus . It is joined also by the least splanchnic nerve. The nerves from these sources, fifteen or twenty in number, have a few ganglia developed upon them. They accompany the branches of the renal artery into the kidney; some filaments are distributed to the spermatic plexus and, on the right side, to the inferior vena cava.
Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers.
The nerve travels through the diaphragm and enters the abdominal cavity, where its fibers synapse at the celiac ganglia. The nerve contributes to the celiac plexus, a network of nerves located in the vicinity of where the celiac trunk branches from the abdominal aorta. The fibers in this nerve modulate the activity of the enteric nervous system of the foregut. They also provide the sympathetic innervation to the adrenal medulla, stimulating catecholamine release.
The nerve travels inferiorly, lateral to the greater splanchnic nerve. Its fibers synapse with their postganglionic counterparts in the superior mesenteric ganglia, or in the aorticorenal ganglion. The nerve modulates the activity of the enteric nervous system of the midgut.
The lumbar splanchnic nerves are splanchnic nerves that arise from the lumbar part of the sympathetic trunk and travel to an adjacent plexus near the aorta. They are originated from L1 and L2. These nerves contain preganglionic sympathetic and visceral afferent fibers. The site of synapse is found in the prevertebral ganglia and innervate the smooth muscle and glands of the pelvic viscera and hindgut.
A splanchnic nerve that connects the inferior hypogastric plexus to the sympathetic trunk in the pelvis.
A mammalian developmental stage that covers the period from birth until weaning.
The meshwork of astrocytic foot processes (glial end feet) covered by a basal lamina adjacent to the inner pial surface of the central nervous system.
A feather that is part of a hindlimb zeugopod.
feather covering of ventral part of tail
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
The dorsal nerve of the penis is the deepest division of the pudendal nerve; it accompanies the internal pudendal artery along the ramus of the ischium; it then runs forward along the margin of the inferior ramus of the pubis, between the superior and inferior layers of the fascia of the urogenital diaphragm. Piercing the inferior layer it gives a branch to the corpus cavernosum penis, and passes forward, in company with the dorsal artery of the penis, between the layers of the suspensory ligament, on to the dorsum of the penis, and ends on the glans penis.
The dorsal nerve of the clitoris is a nerve in females that branches off the pudendal nerve to innervate the clitoris.
Zone of skin that is part of the anterior region of the chest
Gemellus muscle that arises from the upper part of the tuberosity of the ischium, immediately below the groove for the Obturator internus tendon. It blends with the lower part of the tendon of the Obturator internus, and is inserted with it into the medial surface of the greater trochanter.
The smaller of the two gemellus muscles that arises from the outer surface of the spine of the ischium, blends with the upper part of the tendon of the Obturator internus, and is inserted with it into the medial surface of the greater trochanter[WP].
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid
the central point on the anterior surface of the lens.
A central point or region on the anterior or posterior surface of the lens
See https://github.com/obophenotype/uberon/issues/599
supcapsular region of anterior region of lens
supcapsular region of posterior region of lens
A white matter that is part of the hindbrain.
A white matter that is part of the forebrain.
A white matter that is part of the myelencephalon.
mesomere 2 (preisthmus or caudal midbrain)
A fiber pathway in the cerebral white matter that connects anterior portions of the temporal lobe with the inferior frontal gyrus and the middle frontal gyrus. It is not readily distinguished in myelin-stained cross-sections (adapted from Brain Info).
uncinate fasciculus of cerebral hemisphere
The interposed nucleus is a deep nucleus of the cerebellum and is composed of the globose nuclei and the emboliform nuclei. It is located in in the roof (dorsal aspect) of the fourth ventricle, lateral to the fastigial nucleus. It receives its afferent supply from the anterior lobe of the cerebellum and sends output via the superior cerebellar peduncle to the red nucleus.
modulates muscle stretch reflexes of proximal limb muscles[WP]
accessory olfactory bulb external plexiform layer
accessory olfactory bulb internal plexiform layer
predominantly white regional part of pontine tegmentum
posterior intralaminar nucleus of the thalamus
The term septohypothalamic nucleus refers to a group of cells located between the lateral septal nucleus and the anterior commissure in the mouse ( Paxinos-2001 ). Some authors regard it as part of the lateral septal nucleus ( Swanson-1998 ).
The initial segment of an olfactory nerve, leaving the central nervous system.
ventrolateral subnucleus of solitary tract
ventrolateral subnucleus of solitary tract, left
nucleus of the solitary tract, ventrolateral part
an oily substance that prevents evaporation of the eye's tear film
provides barrier to prevent dessication of cornea[ISBN10:0123813611]
part of surface lipid layer of tear film
An exocrine gland that is part of a integumental system.
A subdivision of the trunk that is comprised of the epigastrium and the anterior lower thorax.
A lacrimal gland located superficially at the lateral canthus, where both the lacrimal gland and Harderian gland ducts open.
A lacrimal gland located subcutaneously at the anteroventral base of the ear adjacent to the parotid gland.
more than 10% of rat exorbital gland appears to be composed of harderian gland-like cells by 22 months of age (Coujard 1974; Sashima et al. 1989).[PMID:7559104]
An anatomical lobe that is part of a lacrimal gland
In humans the lacrimal gland consists of two contiguous lobes [ISBN10:0123813611]
Larger of the two lacrimal gland lobes located superficially.
Smaller of the two lacrimal gland lobes located at the eyelid.
accessory nucleus of anterior column of spinal cord
nucleus accessorius columnae anterioris medullae spinalis
See also: http://en.wikipedia.org/wiki/Spinal_accessory_nucleus
A blood vessel that supplies or drains an ear.
The superior longitudinal fasciculus (also called the superior longitudinal fascicle or SLF) is a pair of long bi-directional bundles of neurons connecting the front and the back of the cerebrum. Each association fiber bundle is lateral to the centrum ovale of a cerebral hemisphere and connects the frontal, occipital, parietal, and temporal lobes. The neurons pass from the frontal lobe through the operculum to the posterior end of the lateral sulcus where numerous neurons radiate into the occipital lobe and other neurons turn downward and forward around the putamen and radiate to anterior portions of the temporal lobe.
The precentral sulcus lies parallel to, and in front of, the central sulcus. (A sulcus is one of the prominent grooves on the surface of the human brain. ) The precentral sulcus divides the inferior, middle, and superior frontal gyri from the precentral gyrus. In the majority of brains, the precentral sulcus is divided into two parts: the inferior precentral sulcus and the superior precentral sulcus. However, the precentral sulcus may also be divided into three parts or form one continuous sulcus.
The subthalamic fasciculus is a tract which connects the subthalamic nucleus and the globus pallidus. It is a bidirectional connection between the GP and the subthalamic nucleus, including (1) fibers running from the GPe to the subthalamic nucleus, and (2) fibers running from the STN back to the GP.
The acoustic radiations or auditory radiations are structures found in the brain, in the ventral cochlear pathway, a part of the auditory system. Lesions to the auditory radiations could be a cause of cortical deafness.
The optic radiation (also known as the geniculo-calcarine tract or as the geniculostriate pathway) is a collection of axons from relay neurons in the lateral geniculate nucleus of the thalamus carrying visual information to the visual cortex (also called striate cortex) along the calcarine fissure. There is one such tract on each side of the brain.
The planum temporale is the cortical area just posterior to the auditory cortex within the Sylvian fissure. It is a triangular region which forms the heart of Wernicke's area, one of the most important functional areas for language. The planum temporale shows a significant asymmetry. In 65% of all individuals the left planum temporale appears to be more developed, while the right planum temporale is more developed in only 10%. In some peoplebs brains, the planum temporale is more than five times larger on the left than on the right, making it the most asymmetrical structure in the brain. This greater size of the left planum temporale compared with the right is already present in the foetus, where it can be observed starting from the 31st week of gestation. This observation strengthens the hypothesis of a genetic predisposition for brain asymmetry.
Corticopontine fibers, commonly referred to as corticobulbar fibers, are projections from the cerebral cortex to the pontine nuclei. Depending upon the lobe of origin, they can be classified as frontopontine fibers, parietopontine fibers, temporopontine fibers and occipitopontine fibers. They are motor fibers that stretch from the precentral gyrus (motor strip) to the nuclei of cranial nerves V (trigenimal), VII (facial) and XII (hypoglossal). These fibers run alongside the corticospinal fibers.
The corticobulbar (or corticonuclear) tract is a white matter pathway connecting the cerebral cortex to the brainstem. The term "bulbar" refers to the brainstem, as "bulb" was a historical term meaning the area currently called the brainstem. The 'bulb' is an archaic term for the medulla oblongata. In clinical usage, it includes the pons as well.
A small cistern-like area of the conjunctiva at the medial angle of the eye, in which the tears collect after bathing the front surface of the eyeball and the conjunctival sac.
A small conical elevation at the basal angle of the lacrimal lake.
The splenic (or left colic) flexure is a sharp bend between the transverse and the descending colon in the left upper quadrant of humans. The left colic flexure is near the spleen, and hence called the splenic flexure. There are two colic flexures in the transverse colon — the other being the hepatic flexure in the right upper quadrant.
Hepatic (or the right colic) flexure is the sharp bend between the ascending and the transverse colon. The right colic flexure is adjacent to the liver, and is therefore also known as the hepatic flexure. Thus, the left colic flexure is also known as the splenic flexure (as it is close to the spleen). The hepatic flexure lies in the right upper quadrant of the abdomen in humans.
A nucleus in the ventral part of the anterior horn of the sacral region of the spinal cord that is the origin of the pudendal nerve.
involved in the maintenance of micturition and defecatory continence, as well as muscular contraction during orgasm.
The neurons in Onuf's nucleus are motoneurons, and like most motoneurons they are characterized by their mulipolarity and large Nissl bodies
epithelium of small intestinal crypt of Lieberkuhn
epithelium of crypt of Lieberkuhn of small intestine
epithelium of crypt of Lieberkuhn of large intestine
A merocrine secretion that is produced by a Harderian gland, containing lipids
in amphibians, chiefly seromucoid with some lipids[PMID:7559104]
in birds, mucoid and lipid[PMID:7559104]
in mammals, predominantly lipid; mucoid secretion restricted to extraglandular duct tissue[PMID:7559104]
in the armadillo and opossum, mucous or serous acini may be present[PMID:7559104]
The diverticulum of the thin roof of the dorsocaudal third ventricle that projects into the stalk of the pineal gland.
the single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland)
in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe
a single large hair, surrounded by neurovascular tissue at the level of the sebaceous gland, with a hair follicle innervated by a hair-tylotrich neuron (CL:1001436), a rapidly acting mechanoreceptor.
A secretion that is produced by a nictitans gland, containing glycoprotein
seromucuous in cattle, cat and dog, elephant [ISBN:1118473523]
An aqueous substance that covers the anterior surface of the eyeball, keeping the cornea wet.
maintenance of the avascular transparent corneal epithelium
The tear film is structurally complex with three distinct layers: a surface lipid layer (0.1–0.2 μm thick), a middle aqueous layer (7–8 μm thick), and an inner mucus layer (30 μm thick)[http://physiologyonline.physiology.org/content/13/2/97]
A two dimensional anatomical structure that corresponds to some structural discontinuity.
The outer surface of an organism or its integumental system.
A nerve that innervates a lower eyelid and is a branch of the infra-orbital branch of the maxillary nerve.
rami palpebrales inferiores nervi infraorbitalis
inferior palpebral branch of infra-orbital nerve
A nerve that innervates an eyelid and is a branch of the infra-orbital branch of the maxillary nerve.
A nerve that innervates an upper eyelid.
The nasociliary nerve is a branch of the ophthalmic nerve. It is intermediate in size between the two other main branches of the ophthalmic nerve, the frontal nerve and the lacrimal nerve, and is more deeply placed.
The long ciliary nerves, two or three in number, are given off from the nasociliary, as it crosses the optic nerve. They accompany the short ciliary nerves from the ciliary ganglion, pierce the posterior part of the sclera, and running forward between it and the choroid, are distributed to the iris and cornea. The long ciliary nerves provide sensory innervation to the eyeball. In addition, they contain sympathetic fibers from the superior cervical ganglion to the dilator pupillC& muscle. The sympathetic fibers to the dilator pupillae muscle mainly travel in the nasociliary nerve but there are also sympathetic fibers in the short ciliary nerves that pass through the ciliary ganglion without forming synapses.
The branches of the ciliary ganglion are the short ciliary nerves. These are delicate filaments, from six to ten in number, which arise from the forepart of the ganglion in two bundles connected with its superior and inferior angles; the lower bundle is the larger. They run forward with the ciliary arteries in a wavy course, one set above and the other below the optic nerve, and are accompanied by the long ciliary nerves from the nasociliary. They pierce the sclera at the back part of the bulb of the eye, pass forward in delicate grooves on the inner surface of the sclera, and are distributed to the Ciliaris muscle, iris, and cornea. The short ciliary nerve contains parasympathetic and sympathetic nerve fibers. The parasympathetics arise from the Edinger-Westphal nucleus and synapse in the ciliary ganglion via the oculomotor nerve, the postganglionic parasympathetics leave the ciliary ganglion in the short ciliary nerve and supply the ciliary body and iris. Sympathetics are provided by the superior cervical ganglion and they reach the ganglion either as branches of the nasociliary nerve or directly from the extension of the plexus on the ophthalmic artery (sympathetic branch to ciliary ganglion). Damage to the short ciliary nerve may result in loss of the pupillary light reflex, or mydriasis.
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
Most superficial layer of the superior colliculus consisting primarily of thin fibers derived primarily from the occipital cortex (Brodal, Neurological Anatomy, 2nd 3d, 1981, pg. 544)
Note that in some lamination schemes, more particularly so in primates, this layer is referred to as layer IV thus resulting in some confusion when compared to the present scheme where the lamina dissecans is referred to layer IV[doi:10.1155/2008/381243]
Surface layer of the olfactory cortex that contains dendrites, fiber systems and a small number of neurons. It has been divided into a superficial part and a deep part.
Middle layer of olfactory cortex lying deep to layer 1 and superficial to layer 3, characterized by a compact layer of cell bodies. It can be divided into a superficial part and a deep part.
Layer of the lateral geniculate nucleus characterized by small cells (adapted from http://en.wikipedia.org/wiki/ https://en.wikipedia.org/wiki/Lateral_geniculate_nucleus)
lateral geniculate nucleus parvocellular layer
dorsal cochlear nucleus pyramidal cell layer
Layer of entorhinal cortex lying superficial to layer 5 and deep to layer 3, that is relatively acellular. (Paxinos, The rat nervous system, Academic Press, 1995, pg 473-474).
the two NIFSTD classes appear to refer to the same structure[doi:10.1155/2008/381243]
This layer is better developed in the medial entorhinal cortex although species differences are apparent[doi:10.1155/2008/381243]
Layer of entorhinal cortex lying superficial to layer 6 and deep to layer 4 characterized by large pyramidal neurons that are darkly stained in Nissl preparations (Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 474)
molecular layer of dorsal cochlear nucleus
Layer of the entorhinal cortex lying superficial to layer 4and deep to layer 2. It is characterized by cells of various sizes and shapes with a predominance of pyramidal cells (Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 474)
Layer of entorhinal cortex lying superficial to the cerebral white matter and deep to layer 5 characterized by cells of various shapes and sizes (Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 474)
This layer is delineated by the white matter, multiple layers can be distinguished, more in particular in primates[doi:10.1155/2008/381243]
Layer of the entorhinal cortex that is most superficial, continuous with layer 1 of adjacent neocortex and the molecular layer of the subiculum, lying deep to the pial layer and superficial to layer 2. It is relatively acellular consisting mostly of fibers running transversely relative to the cortical surface (Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 474)
superficial plexiform layer of entorhinal cortex
Layer of the entorhinal cortex lying superficial to layer 3 and deep to layer 1. It is characterized by medium-to large sized stellate cells that are grouped into prominent clusters, particularly in the rostral entorhinal cortex (Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 474)
outermost cell layer of entorhinal cortex
Superficial region of layer 2 of the piriform cortex characterized by a less dense packing of cells and a concentration of semilunar cell bodies
Deeper of two subdivisions of piriform layer 2 characterized by more densely packed cell bodies dominated by pyramidal cell bodies.
middle layer of dentate gyrus molecular layer
inner layer of dentate gyrus molecular layer
extrapyramidal blade dentate gyrus granule cell layer
extrapyramidal blade of stratum granulare
inner blade of dentate gyrus granule cell layer
dentate gyrus granule cell layer inner blade
infrapyramidal blade dentate gyrus granule cell layer
infrapyramidal blade of stratum granulare
outer blade of dentate gyrus granule cell layer
dentate gyrus granule cell layer outer blade
Component of the orbtial frontal cortex. The rostral boundary is the first slice where the medial orbital gyrus became visible whereas the caudal boundary is the disappearance of the medial orbital gyrus/gyrus rectus. The medial and lateral boundaries are the cingulate cortex on the u2018inflatedu2019 surface and the medial bank of the superior frontal gyrus (or the cingulate gyrus when visible) respectively (Christine Fennema-Notestine).
Component of the cingulate cortex. The rostral and caudal extent were the caudal anterior and the isthmus divisions of the cingulate cortex respectively. The medial and lateral boundaries were the corpus callosum and as the superior frontal gyrus and/or paracentral lobule respectively (Christine Fennema-Notestine).
check relationship to gyrus. See https://github.com/obophenotype/uberon/issues/626
The layer of endometrial epithelium adjacent to the uterine cavity.
The layer of endometrial epithelium adjacent to the myometrium.
A mammary gland duct that is part of a male organism. This structure typically regresses.
A specific region of the foregut into the area in which the lung will develop.
occipitotemporal (fusiform) gyrus, occipital part
lateral occipital cortex, inferior division
lateral occipital cortex, inferior division (OLI)
lateral occipital cortex, superior division
parahippocampal gyrus, anterior division
substantia medullaris parahippocampalis posterior
occipitotemporal (fusiform) gyrus, temporal part
occipitotemporal (fusiform) gyrus, anterior division
occipitotemporal (fusiform) gyrus, posterior division
superior longitudinal fasciculus, temporal division
temporal part of superior longitudinal fasciculus
Part of the superior olivary complex of nuclei in the caudal pontine tegmentum, situated within the trapezoid body in humans. (Brodal, Neurological Anatomy, 3rd edition, 1981, pg 617). In many species, it comprises a medial superior olivary nucleus and a lateral superior olivary nucleus.
Wikipedia includes Medial nucleus of the trapezoid body. http://en.wikipedia.org/wiki/Superior_olivary_complex#Primary_nuclei
many sources refer to this simply as the 'superior olive' or the 'superior olivary nucleus'. However, this is confusing as superior olive is sometimes used to denote the full SOC, which includes periolvary nuclei[https://github.com/obophenotype/uberon/issues/631]
Component of the cingulate cortex. The rostral boundary was the first appearance of the cingulate sulcus (inferior to the superior frontal sulcus) whereas the caudal boundary was the first appearance of the genu of the corpus callosum. The medial boundary was the medial aspect of the cortex. The supero-lateral boundary was the superior frontal gyrus whereas the infero-lateral boundary was defined as the medial division of the orbitofrontal gyrus (Christine Fennema-Notestine).
A part of the entorhinal area defined on the basis of connectivity. It is the rostral portion, which receives a projection from the olfactory bulb (Price-90)-Adapted from Brain Info
The term primary olfactory areas in the primate, refers to a group of structures defined by connectivity, namely, structures that receive axons from the olfactory bulb. They include the anterior olfactory nucleus, the anterior perforated substance, the rostral part of the medial amygdaloid nucleus (anterior cortical nucleus of amygdala), and structures in the anterior part of the parahippocampal gyrus, namely, the prepyriform area, most of the periamygdaloid area, and the rostral part of the entorhinal area (Price-90). Note that some authors have regarded the olfactory bulb itself as the primary olfactory area and the areas to which it projects as secondary (Anthoney-94). In the mouse (Dong-2004) and the rat (Swanson-2004), olfactory areas include the olfactory bulb, accessory olfactory bulb, anterior olfactory nucleus, tenia tecta, prepyriform area, postpiriform transition area, piriform amygdaloid area, nucleus of lateral olfactory tract, and cortical amygdaloid area.
predominantly gray regional part of pretectal region
obsolete predominantly gray regional part of pretectal region
Component of the parietal lobe. The rostral boundary of the pericalcarine cortex was the first appearance of the calcarine sulcus whereas the caudal boundary was the most posterior coronal slice where the calcarine sulcus was visualized. The medial and lateral boundaries were the medial portion of the temporal and occipital cortices and the inferomedial end of the calcarine sulcus respectively (Christine Fennema-Notestine).
obsolete regional part of solitary nucleus
regional part of a lobe of the cerebellum
regional part of peripheral nervous system
obsolete regional part of peripheral nervous system
predominantly gray regional part of epithalamus
obsolete predominantly gray regional part of epithalamus
habenulo-interpeduncular tract of diencephalon
obsolete regional part of occipital lobe
predominantly gray regional part of lateral hypothalamic region
obsolete predominantly gray regional part of lateral hypothalamic region
obsolete regional part of cerebral peduncle
predominantly gray regional part of posterior hypothalamic region
obsolete predominantly gray regional part of posterior hypothalamic region
Component of the orbtial frontal cortex The rostral boundary is the first slice where the lateral orbital gyrus is apparent with the frontomarginal sulcus whereas the caudal boundary is the disappearance of the lateral orbital gyrus. The medial and lateral boundaries are the midpoint of the olfactory sulcus and the lateral bank of the lateral orbital sulcus and/or the circular insular sulcus respectively (Christine Fennema-Notestine).
superficial feature part of midbrain tectum
obsolete superficial feature part of midbrain tectum
obsolete regional part of central nervous system
superficial feature part of intermediate hypothalamic region
obsolete superficial feature part of intermediate hypothalamic region
composite part spanning multiple base regional parts of brain
regional part of medial mammillary nucleus
obsolete regional part of medial mammillary nucleus
paraventricular nucleus of the hypothalamus magnocellular division - posterior magnocellular part medial zone
paraventricular nucleus of the hypothalamus magnocellular division - posterior magnocellular part lateral zone
superficial feature part of diencephalon
obsolete superficial feature part of diencephalon
predominantly gray regional part of medullary raphe nuclear complex
obsolete predominantly gray regional part of medullary raphe nuclear complex
regional part of oculomotor nuclear complex
obsolete regional part of oculomotor nuclear complex
predominantly gray regional part of midbrain tegmentum
obsolete predominantly gray regional part of midbrain tegmentum
posterior nerve root of sacral spinal cord
predominantly white regional part of midbrain tegmentum
obsolete predominantly white regional part of midbrain tegmentum
regional part of midbrain reticular formation
obsolete regional part of midbrain reticular formation
superficial feature part of medulla oblongata
obsolete superficial feature part of medulla oblongata
predominantly white regional part of posterior hypothalamic region
obsolete predominantly white regional part of posterior hypothalamic region
superficial feature part of posterior hypothalamic region
obsolete superficial feature part of posterior hypothalamic region
predominantly white regional part of septum pellucidum
obsolete predominantly white regional part of septum pellucidum
obsolete regional part of cerebral white matter
predominantly white regional part of epithalamus
obsolete predominantly white regional part of epithalamus
posterodorsal nucleus of medial geniculate body
nucleus corporis geniculati medialis, pars posterodorsalis
posterodorsal nucleus of medial geniculate complex
predominantly gray regional part of intermediate hypothalamic region
obsolete predominantly gray regional part of intermediate hypothalamic region
predominantly gray regional part of hypothalamus
obsolete predominantly gray regional part of hypothalamus
cytoarchitectural part of cerebral cortex
obsolete cytoarchitectural part of cerebral cortex
regional part of ventral cochlear nucleus
obsolete regional part of ventral cochlear nucleus
predominantly gray part of medulla oblongata
obsolete predominantly gray part of medulla oblongata
solitary nucleus, left, meidal subnucleus
regional part of spinal cord dorsal horn
regional part of spinal cord gray commissure
lateral amygdaloid nucleus, dorsolateral part
lateral amygdaloid nucleus, ventrolateral part
lateral amygdaloid nucleus, ventromedial part
superficial feature part of occipital lobe
regional part of stratum pyramidale hippocampi
obsolete regional part of stratum pyramidale hippocampi
obsolete regional part of stratum oriens
obsolete regional part of stratum radiatum
regional part of stratum lacunosum moleculare
obsolete regional part of stratum lacunosum moleculare
obsolete regional part of basal nuclear complex
predominantly gray regional part of inferior colliculus
obsolete predominantly gray regional part of inferior colliculus
ventral nerve root of sacral spinal cord
anterior nerve root of sacral spinal cord
regional part of anterior hypothalamic region
obsolete regional part of anterior hypothalamic region
regional part of granular layer of cerebellar cortex
obsolete regional part of granular layer of cerebellar cortex
predominantly white regional part of hypothalamus
obsolete predominantly white regional part of hypothalamus
predominantly white regional part of tectum
obsolete predominantly white regional part of tectum
predominantly gray regional part of tectum
obsolete predominantly gray regional part of tectum
obsolete regional part of septal nuclear complex
superficial feature part of telencephalon
obsolete superficial feature part of telencephalon
habenulo-interpeduncular tract of midbrain
gross anatomical part of cerebral cortex
obsolete gross anatomical part of cerebral cortex
A composite structure of the temporal lobe that includes the subiculum, the presubiculum and the parasubicular area (Amaral-90)
predominantly white regional part of inferior colliculus
obsolete predominantly white regional part of inferior colliculus
cytoarchitectural part of the cerebellum
obsolete cytoarchitectural part of the cerebellum
gross anatomical parts of the cerebellum
an area of the brain that locates at the interception of temporal and parietal cortices (at the posterior end of the Sylvian fissure).
commissural nucleus of the solitary tract
A portion of the superior temporal gyrus near the temporal pole in the human.
The combined region of AmmonÕs horn, subicular complex and dentate gyrus; only fields CA1-CA3 of the hippocampus were considered to be part of the HF, field CA4 being included in the hilus of the dentate gyrus[1]
Part of olfactory tubercle defined by dense aggregations of granule cells
islands of calleja of olfactory tubercle
Regional part of telencephalon; the most prominent of the islands of Calleja located medially in the nucleus accumbens (adapted from Braininfo.org).
Part of body that takes the form of a thin sheet of cells or fibrous material, e.g., the meningeal coverings of the brain.
Not sure this is the correct designation; FMA has "membranous organ" but that doesn't seem quite right either.
A set of neural structures that subserve a specific function, e.g., visual system
Superficial part of plexiform layer (layer 1) of piriform cortex that receives afferents from the olfactory bulb by way of the lateral olfactory tract.
Deeper part of the plexiform (layer 1) of piriform cortex characterized by projection of association fibers from other parts of the piriform cortex and other olfactory areas
subbrachial nucleus of mouse of franklin and paxinos 2008
Cortical region lying caudal to the perirhinal cortex in the rat. It encompasses the caudal levels of area 35 and the caudal portion of area 36 (ectorhinal cortex). It is bordered medially by agranular retrosplenial cortex and ventrally by the entorhinal cortex (with the exception of the caudomedial portion). The authors note that the ventral portion of the postrhinal cortex in rat may by homologous with the parahippocampal cortex in the monkey.
postrhinal cortex of rodent of burwell et al 1995
Part of hippocampal formation comprising area CA1 and the subiculum (pg 425, Heimer, L. The human brain and spinal cord, Springer-Verlag, 1995)
The glomerular layer of the main olfactory bulb, lying deep to the olfactory nerve layer. It contains the glomeruli, neuropil rich spheroid structures surrounded by a distinctive shell of small neuros and glial cells (Paxinos, the Rat Nervous System, 2nd ed., Academic Press, 1995).
Rostral portion of the parahippocampal cortex
Part of bed nucleus of stria terminalis, comprising a distinct, large, egg-shaped collection of neurons that, together with the juxtacapsular (Ju) and rhomboid (Rh) nuclei, encompass the anterolateral area of the BST (Ju and Swanson, 1989)
bed nuclei of the stria terminalis oval nucleus
Originates from cells rostral to Clarke's column and sends uncrossed axons through the lateral funiculus to the cerebellum. It reaches the cerebellum partly through the brachium conjunctivum and partly through the restiform body, terminating bilaterally in the anterior lobe of the cerebellum
vermis of the flocculonodular lobe of the cerebellum
rostral portion of the medial accessory olive
White matter that lies deep to the granular cell layer of the cerebellar cortex. It contains afferents to the cerebellar cortex and axons that run between the cerebellar cortex and the deep cerebellar nuclei.
superficial feature part of the cerebellum
obsolete regional part of nucleus accumbens
One of two divisions of the supraoptic nucleus observed in mammals, formed by the ascension of the optic chiasm to split the nucleus in two. The principal anterior division consists of a dense cluster of large cells that stain darkly in Nissl preparations adjacent to the optic chiasm, extending as far rostrally to the organum vasculosum of the lamina terminalis and caudally into the posterior hypothalamus.
principal anterior division of supraoptic nucleus
Posterior division of the supraoptic nucleus, formed by the ascension of the optic tract splitting the nucleus into two regions. The tuberal SON lies along the posterior tuber cinereum of the hypothalamus. In some species, some neurons lie under the optic chiasm.
obsolete regional part of stratum lucidum
cytoarchitectural part of dorsal tegmental nucleus
obsolete cytoarchitectural part of dorsal tegmental nucleus
Regional part of an anatomical region that is revealed by the use of a stain that reveals chemoarchitecture.
obsolete regional part of adenohypophysis
The ventral topographic division of the midbrain; the dorsal topographic division is the tectum. Meckel (1817; see English translation, 1832, vol. 2, p. 467) apparently introduced the term and roughly its definition here for macrodissected adult humans, except he excluded the cerebral peduncle (Tarin, 1753), a white matter tract at the base of the midbrain, which is still common today but is included here. As defined here, tegmentum refers to the whole of the midbrain (Baer, 1837) excluding the tectum but including the pretectal region (Scalia, 1972); see Swanson (2000, pp. 522, 526). Usage of this term is very complex, inconsistent, and illogical; see for example Crosby et al. (1962, pp. 221, 260, 262), Carpenter (1976, p. 367 ff.).
obsolete regional part of pontine tegmentum
superficial feature part of cerebral cortex
obsolete superficial feature part of cerebral cortex
predominantly white regional part of cerebellar cortex
obsolete predominantly white regional part of cerebellar cortex
predominantly gray regional part of frontal lobe
obsolete predominantly gray regional part of frontal lobe
regional part of deep cerebellar nuclear complex
obsolete regional part of deep cerebellar nuclear complex
regional part of autonomic nervous system
obsolete regional part of autonomic nervous system
obsolete regional part of basal part of pons
predominantly gray regional part of parietal lobe
obsolete predominantly gray regional part of parietal lobe
predominantly gray regional part of anterior hypothalamic region
obsolete predominantly gray regional part of anterior hypothalamic region
predominantly white regional part of cerebral peduncle
obsolete predominantly white regional part of cerebral peduncle
predominantly white regional part of anterior hypothalamic region
obsolete predominantly white regional part of anterior hypothalamic region
obsolete regional part of orbital gyri complex
regional part of transverse frontopolar gyri complex
obsolete regional part of transverse frontopolar gyri complex
ventral nerve root of lumbar spinal cord
anterior nerve root of lumbar spinal cord
obsolete regional part of Parahippocampal gyrus
regional part of tuberomammillary nucleus
obsolete regional part of tuberomammillary nucleus
predominantly gray regional part of medial mammillary nucleus
obsolete predominantly gray regional part of medial mammillary nucleus
superficial feature part of frontal lobe
obsolete superficial feature part of frontal lobe
hemispheric parts of the cerebellar cortex
regional part of inferior parietal cortex
obsolete regional part of inferior parietal cortex
predominantly gray regional part of occipital lobe
obsolete predominantly gray regional part of occipital lobe
obsolete regional part of neuraxis cavity
predominantly gray regional part of midbrain reticular formation
obsolete predominantly gray regional part of midbrain reticular formation
predominantly gray regional part of oculomotor nuclear complex
obsolete predominantly gray regional part of oculomotor nuclear complex
predominantly gray regional part of red nucleus
obsolete predominantly gray regional part of red nucleus
predominantly white regional part of red nucleus
obsolete predominantly white regional part of red nucleus
predominantly gray regional part of habenula
obsolete predominantly gray regional part of habenula
regional part of sacral spinal cord white matter
predominantly gray regional part of basal nuclear complex
obsolete predominantly gray regional part of basal nuclear complex
superficial feature part of temporal lobe
obsolete superficial feature part of temporal lobe
obsolete superficial feature part of hypophysis
obsolete regional part of cingulate gyrus
predominantly gray regional part of temporal lobe
obsolete predominantly gray regional part of temporal lobe
regional part of lumbar spinal cord white matter
predominantly gray regional part of thalamus
obsolete predominantly gray regional part of thalamus
predominantly white regional part of thalamus
obsolete predominantly white regional part of thalamus
A collection of neuronal components interacting in a functional circuit. A neural circuit is bounded by the nervous sytem regions in which its participating neuronal components are contained (BB).
ganglion part of peripheral nervous system
predominantly gray part of ventral cochlear nucleus
obsolete predominantly gray part of ventral cochlear nucleus
predominantly gray part of solitary nucleus
obsolete predominantly gray part of solitary nucleus
regional part of corticomedial nuclear complex
obsolete regional part of corticomedial nuclear complex
obsolete regional part of olfactory cortex
superficial feature part of parietal cortex
obsolete regional part of longitudinal fissure
cytoarchitectural part of occipital lobe
obsolete cytoarchitectural part of occipital lobe
obsolete cytoarchitectural part of frontal lobe
regional part of cervical spinal cord white matter
predominantly white regional part of fornix
obsolete predominantly white regional part of fornix
obsolete regional part of anterior commissure
obsolete regional part of hippocampal formation
obsolete regional part of substantia nigra
obsolete regional part of inferior frontal gyrus
predominantly gray regional part of limbic lobe
obsolete predominantly gray regional part of limbic lobe
predominantly gray regional part of septal nuclear complex
obsolete predominantly gray regional part of septal nuclear complex
obsolete regional part of neurohypophysis
obsolete regional part of cingulate cortex
regional part of thoracic spinal cord gray matter
The sensory system for the sense of proprioception.
Cortical region near the rhinal sulcus in primate encompassing Brodmann's areas 35 and 36
perirhinal cortex of primate of burwell et al 1995
Cortical region surrounding the posterior rhinal sulcus in the rat, encompassing areas 35 and 36 in the rat. Rostraly, it abuts the posterior insular cortex
perirhinal cortex of rodent of burwell et al 1995
any molecule, protein, cell, tissue or organ that is related to histamine.
any molecule, protein, cell, tissue or organ that is related to the catecholamines.
any molecule, protein, cell, tissue or organ that is related to GABA.
any molecule, protein, cell, tissue or organ that is related to glutamate (when in the role of a neurotransmitter).
any molecule, protein, cell, tissue or organ that is related to serotonin.
any molecule, protein, cell, tissue or organ that is related to acetylcholine.
Part of brain and spinal cord excluding retina.
paravermis parts of the cerebellar cortex
regional part of dorsal cochlear nucleus
obsolete regional part of dorsal cochlear nucleus
predominantly gray regional part of adenohypophysis
obsolete predominantly gray regional part of adenohypophysis
predominantly white regional part of basal part of pons
obsolete predominantly white regional part of basal part of pons
predominantly gray regional part of pontine tegmentum
obsolete predominantly gray regional part of pontine tegmentum
regional part of pontine reticular formation
obsolete regional part of pontine reticular formation
regional part of superior olivary complex
obsolete regional part of superior olivary complex
regional part of anterior nucleus of hypothalamus
obsolete regional part of anterior nucleus of hypothalamus
predominantly white regional part of hippocampal formation
obsolete predominantly white regional part of hippocampal formation
Sulcus in the frontal lobe of the macaque. (Brain Info)
obsolete regional part of enteric nervous system
predominantly gray regional part of basal part of pons
obsolete predominantly gray regional part of basal part of pons
obsolete regional part of dentate nucleus
obsolete regional part of hippocampus proper
predominantly gray regional part of orbital gyri complex
obsolete predominantly gray regional part of orbital gyri complex
predominantly gray medial regional part of thalamus
obsolete predominantly gray medial regional part of thalamus
regional part of cerebral ventricular cavity
obsolete regional part of cerebral ventricular cavity
obsolete regional part of median eminence
posterior nerve root of lumbar spinal cord
predominantly gray regional part of transverse frontopolar gyri complex
obsolete predominantly gray regional part of transverse frontopolar gyri complex
predominantly gray regional part of parahippocampal gyrus
obsolete predominantly gray regional part of Parahippocampal gyrus
predominantly gray dorsal regional part of thalamus
obsolete predominantly gray dorsal regional part of thalamus
predominantly white dorsal regional part of thalamus
obsolete predominantly white dorsal regional part of thalamus
obsolete regional part of middle frontal gyrus
regional part of paravsuprachiasmatic nucleus
regional part of suprachiasmatic nucleus
obsolete regional part of suprachiasmatic nucleus
superficial feature part of cerebral peduncle
obsolete superficial feature part of cerebral peduncle
predominantly gray regional part of inferior parietal cortex
obsolete predominantly Gray regional part of inferior parietal cortex
regional part of paraventricular nucleus of hypothalamus
obsolete regional part of paraventricular nucleus of hypothalamus
predominantly gray anterior regional part of thalamus
obsolete predominantly gray anterior regional part of thalamus
regional part of cervical spinal cord gray matter
predominantly gray regional part of cingulate gyrus
obsolete predominantly gray regional part of cingulate gyrus
regional part of transverse temporal cortex
obsolete regional part of transverse temporal cortex
predominantly gray ventral regional part of thalamus
obsolete predominantly gray ventral regional part of thalamus
predominantly gray posterior regional part of thalamus
obsolete predominantly gray posterior regional part of thalamus
dorsomedial subnucleus of solitary tract
nucleus of the solitary tract, dorsomedial part
A neuronal circuit bearing a principal projection neuron whose axon extends beyond the region where its soma is located to synapse on the dendrites of cells in other regions of the nervous system (BB).
A neuronal circuit where all the participating neurons are bounded within a defined and limited region of the nervous system.(BB).
spinal ganglion part of peripheral nervous system
dorsolateral subnucleus of solitary tract
nucleus of the solitary tract, dorsolateral part
parvicellular subnucleus of solitary tract
regional part of basolateral nuclear complex
obsolete regional part of basolateral nuclear complex
predominantly gray part of corticomedial nuclear complex
obsolete predominantly gray part of corticomedial nuclear complex
regional part of posterior superior frontal sulcus
obsolete regional part of posterior superior frontal sulcus
The term medial precentral sulcus (H) refers to a superficial feature of the frontal lobe that extends from the dorsal surface onto the medial surface of the superior frontal gyrus (Ono-90). (NN)
The term transverse parietal sulcus (H) refers to a sulcus in the human PARIETAL LOBE that branches dorsally from the intraparietal sulcus (Savel'ev-96). (NN)
The term superior parietal sulcus (H) refers to a superficial feature of the parietal lobe that extends from the dorsal surface of the superior parietal lobule across the margin of the parietal lobe into the precuneus (Ono-90). (NN)
The term angular sulcus (H) refers to a superficial feature of the parietal lobe. It is the portion of the superior temporal sulcus that extends into the angular gyrus (Ono-90). (NN)
obsolete regional part of calcarine sulcus
hadjikhani et al. (1998) visuotopic partition scheme region
hadjikhani visuotopic parcellation scheme
Cortical parcel in occipital cortex of human according to Tootell and Hadjikhani 2001 that is activated preferentially by more peripheral stimuli compared to the adjacent lateral occipital central parcel
tootell and hadjikhani (2001) loc/lop complex
press, brewer, dougherty, wade and wandell (2001) visuotopic area v7
ongur, price, and ferry (2003) prefrontal cortical partition scheme region
ongur, price, and ferry (2003) prefrontal cortical areas
ongur, price, and ferry (2003) prefrontal cortical parcellation scheme
ongur, price, and ferry (2003) prefrontal cortical partition scheme
predominantly gray regional part of preoptic area
obsolete predominantly gray regional part of Preoptic area
predominantly gray regional part of substantia nigra
obsolete predominantly gray regional part of substantia nigra
predominantly gray regional part of inferior frontal gyrus
obsolete predominantly gray regional part of inferior frontal gyrus
predominantly white regional part of anterior commissure
obsolete predominantly white regional part of anterior commissure
predominantly gray midline regional part of thalamus
obsolete predominantly gray midline regional part of thalamus
regional part of superior temporal sulcus
obsolete regional part of superior temporal sulcus
regional part of thoracic spinal cord white matter
predominantly gray regional part of neurohypophysis
obsolete predominantly gray regional part of neurohypophysis
regional part of anterior cingulate cortex
obsolete regional part of Anterior cingulate cortex
predominantly gray intralaminal regional part of thalamus
obsolete predominantly gray intralaminal regional part of thalamus
regional part of cerebellar peduncular complex
obsolete regional part of cerebellar peduncular complex
predominantly gray lateral regional part of thalamus
obsolete predominantly gray lateral regional part of thalamus
any molecule, protein, cell, tissue or organ that is related to epinephrine (also known as adrenaline).
any molecule, protein, cell, tissue or organ that is related to norepinephrine (also known as noradrenaline).
obsolete cytoarchitectural part of retina
any molecule, protein, cell, tissue or organ that is related to dopamine.
obsolete matrix part of body of caudate nucleus
striosomal part of body of caudate nucleus
Matrix compartment located in the head of the caudate nucleus
Matrix compartment located in the tail of the caudate nucleus
striosomal part of tail of caudate nucleus
obsolete striosomal part of tail of caudate nucleus
regional parts of the paravermal lobules
paravermis of the posterior lobe of the cerebellum
paravermis of the anterior lobe of the cerebellum
regional parts of the interpositus nucleus
hemispheric part of the flocculonodular lobe of the cerebellum
The white matter contained within the cerebellum, lying deep to the granule cell layer in the cerebellar cortex, excluding the parts of the cerebellar peduncles that extend outside of the cerebellum. The deep cerebellar nuclei are embedded within the arbor vitae.
obsolete regional part of supraoptic nucleus
The larger of two chemoarchitectural compartments identified in the neostriatum through differential staining for various biochemical markers. It usually is identified through differentially high staining for acetylcholinesterase and calbinin D28K.
One of two compartments identified in the neostriatum, particularly the caudate nucleus, on the basis of differential staining for several biochemical markers such as acetylcholinesterase and calbindin. In individual sections, the striosomes appear as small patches of differentially high or low staining activity. In three dimensions, they form a 3D labyrinth extending throughout the caudate nucleus and in the putamen.
cytoarchitectural part of dorsal cochlear nucleus
granule cell layer of dorsal cochlear nucleus
obsolete cytoarchitectural part of dorsal cochlear nucleus
predominantly gray regional part of dentate nucleus
obsolete predominantly gray regional part of dentate nucleus
predominantly gray regional part of pontine reticular formation
obsolete predominantly gray regional part of pontine reticular formation
predominantly gray regional part of dentate gyrus
obsolete predominantly gray regional part of dentate gyrus
obsolete regional part of caudate nucleus
predominantly gray regional part of neostriatum
obsolete predominantly gray regional part of neostriatum
obsolete regional part of globus pallidus
predominantly gray regional part of ventral nuclear group
obsolete predominantly gray regional part of ventral nuclear group
predominantly gray regional part of medial dorsal nucleus
obsolete predominantly gray regional part of medial dorsal nucleus
obsolete regional part of lateral ventricle
predominantly gray regional part of median eminence
obsolete predominantly gray regional part of median eminence
predominantly gray regional part of metathalamus
obsolete predominantly gray regional part of metathalamus
predominantly white dorsal regional part of metathalamus
obsolete predominantly white dorsal regional part of metathalamus
predominantly gray regional part of anterior nuclear group
obsolete predominantly gray regional part of anterior nuclear group
predominantly gray regional part of superior olivary complex
obsolete predominantly gray regional part of superior olivary complex
predominantly white regional part of superior olivary complex
obsolete predominantly white regional part of superior olivary complex
regional part of paraventricular nucleus of hypothalamus magnocellular division
obsolete regional part of paraventricular nucleus of hypothalamus magnocellular division
obsolete regional part of superior olive
suprachiasmatic nucleus dorsomedial part
suprachiasmatic nucleus ventrolateral part
regional part of thoracic spinal cord dorsal horn
regional part of paraventricular nucleus of hypothalamus descending division
obsolete regional part of paraventricular nucleus of hypothalamus descending division
predominantly gray regional part of hippocampal formation
obsolete predominantly gray regional part of hippocampal formation
regional part of sacral spinal cord gray matter
regional part of lumbar spinal cord gray matter
regional part of cervical spinal cord dorsal horn
obsolete regional part of spiral organ of Corti
predominantly gray regional part of amygdala
obsolete predominantly gray regional part of amygdala
predominantly gray part of basolateral nuclear complex
obsolete predominantly gray part of basolateral nuclear complex
regional part of basal amygdaloid nucleus
obsolete regional part of basal amygdaloid nucleus
obsolete regional part of entorhinal cortex
hadjikhani et al. (1998) visuotopic area v1d
hadjikhani et al. (1998) visuotopic area v1v
hadjikhani et al. (1998) visuotopic area v2v
hadjikhani et al. (1998) visuotopic area v3
hadjikhani et al. (1998) visuotopic area v3a
hadjikhani et al. (1998) visuotopic area vp
hadjikhani et al. (1998) visuotopic area v4v
hadjikhani et al. (1998) visuotopic area v8
Area 10m is a cortical area in the frontal lobe defined on multiple architectonic criteria.
ongur, price, and ferry (2003) area prco
ongur, price, and ferry (2003) area iapm
predominantly gray part of posterior nuclear complex
obsolete predominantly gray part of posterior nuclear complex
predominantly gray part of intralaminar nuclear group
obsolete predominantly gray part of Intralaminar nuclear group
predominantly gray regional part of midline nuclear group
obsolete predominantly gray regional part of midline nuclear group
Component of the temporal lobe, lateral aspect. The rostral boundary is the superior temporal gyrus and the caudal boundary the middle temporal gyrus. Within the FreeSurfer definition, this reflects primarily the posterior aspect of the superior temporal sulcus (Christine Fennema-Notestine).
Component of the cingulate cortex. The rostral boundary was the first appearance of the genu of the corpus callosum whereas the caudal boundary was established as the first appearance of the mammillary bodies. The medial boundary was the medial aspect of the cortex. The supero-lateral boundary was the superior frontal gyrus whereas the infero-lateral boundary was the corpus callosum (Christine Fennema-Notestine).
regional part of substantia nigra pars reticulata
obsolete regional part of substantia nigra pars reticulata
predominantly gray regional part of lateral nuclear group
obsolete predominantly gray regional part of lateral nuclear group
Matrix compartment located in the caudate nucleus
granular cell layer of dorsal cochlear nucleus
predominantly gray regional part of ventral lateral nucleus
obsolete predominantly gray regional part of ventral lateral nucleus
predominantly white dorsal regional part of medial geniculate body
obsolete predominantly white dorsal regional part of medial geniculate body
predominantly gray regional part of superior olive
obsolete predominantly gray regional part of superior olive
regional part of paraventricular nucleus of hypothalamus magnocellular division - posterior magnocellular part
obsolete regional part of paraventricular nucleus of hypothalamus magnocellular division - posterior magnocellular part
predominantly gray regional part of lateral geniculate body
obsolete predominantly gray regional part of lateral geniculate body
predominantly gray regional part of medial geniculate body
obsolete predominantly gray regional part of medial geniculate body
predominantly white regional part of globus pallidus
obsolete predominantly white regional part of globus pallidus
predominantly gray regional part of ventral posterior nucleus
obsolete predominantly gray regional part of ventral posterior nucleus
obsolete regional part of basilar membrane
regional part of trapezoid nuclear complex
obsolete regional part of trapezoid nuclear complex
regional part of lateral amygdaloid nucleus
obsolete regional part of lateral amygdaloid nucleus
predominantly gray part of basal amygdaloid nucleus
obsolete predominantly gray part of basal amygdaloid nucleus
predominantly gray regional part of ventral anterior nucleus
obsolete predominantly gray regional part of ventral anterior nucleus
predominantly gray regional part of pulvinar
obsolete predominantly gray regional part of pulvinar
predominantly gray part of rostral intralaminar nuclei
obsolete predominantly gray part of rostral intralaminar nuclei
predominantly gray regional part of globus pallidus
obsolete predominantly gray regional part of globus pallidus
predominantly gray regional part of ventral posterolateral nucleus
obsolete predominantly gray regional part of ventral posterolateral nucleus
predominantly gray regional part of ventral posteromedial nucleus
obsolete predominantly gray regional part of ventral posteromedial nucleus
regional part of lumbar spinal cord dorsal horn
A taste bud that is located on the soft palate, in the roof of the mouth.
Composite sulcus of the frontal lobe of the macaque. Located on the dorsolateral surface, it consists of the superior ramus of the arcuate sulcus (macaque), the inferior ramus of the arcuate sulcus and the spur of the arcuate sulcus (macaque) (http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2379)
A cytoarchitecturally defined portion of the periamygdalar area and the cortical amygdalar nucleus at the caudal extreme of the amygdala.
All authors regard it as occupying the caudal third of the amygdala, which abuts the hippocampal formation. In the human ( Mai-1997 ) and the macaque ( Amaral-1992 ) it is located close to the medial surface of the temporal lobe; it is bounded internally by the posterior cortical amygdalar nucleus and the temporal horn of the lateral ventricle. In the rat ( Swanson-2004 ) and mouse ( Hof-2000 ) it is bounded largely by the posterior cortical amygdalar nucleus and the accessory basal nucleus (known as the basomedial nucleus of the amygdala in rodents); the stria terminalis separates it from the ventricle. According to some authors the amygdalohippocampal area extends anteriorly to occupy the caudal half of the amygdala. These authors divide the area into two or three parts, which in the human ( Olmos-2004 ), the rat ( Paxinos-2009b ), and the mouse ( Franklin-2008 ) are named on the basis of location: anterolateral, posterolateral and posteromedial parts. In the macaque ( Paxinos-2009a ) the rostral portion of the area is divided into two parts on the basis of cellular morphology: magnocellular and parvicellular parts. Some authors refer to the area in rodents as the 'posterior amygdalar nucleus' ( Swanson-2004; Hof-2000 ).[http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2028]
corpus callosum, posterior forceps (Arnold)
posterior forceps of the corpus callosum
corpus callosum, anterior forceps (Arnold)
A zone of thyroid cartilage formed by fusion of the two plate-like laminae of the cartilages.
Any organ that is the primary organ of vocalization behavior. Examples: The laryngeal vocal cord (humans), the syrinx (birds).
A thin membrane, prolonged downward around the surface of the spermatic cord and testis. It is separated from the dartos tunic by loose areolar tissue. It is derived from the aponeurosis of the abdominal external oblique muscle.
The cremasteric artery (external spermatic artery) is a branch of the Inferior epigastric artery which accompanies the spermatic cord, and supplies the Cremaster and other coverings of the cord, anastomosing with the testicular artery (internal spermatic artery in older texts). (In the female, the cremesteric artery is very small and accompanies the round ligament.)
cremasteric part of inferior epigastric artery
The portion of the gubernacular bulb that is located within the abdomen.
The portion of the gubernacular bulb that is located external to the abdomen.
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047]
spinal cord lateral wall ventricular layer
The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate.
fibrocartilage containing bundles of yellow elastic fibers but with little or no white fibrous tissue.
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain
A cranial nerve fiber tract that innervates the parietal eye.
This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN10:0471888893]
A cranial nerve fiber tract that innervates the pineal body.
The more rostral of the two branches of the epiphyseal tract.
A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish.
A taste bud that is located on a barbel.
A taste bud that is located on the skin of the head.
A taste bud that is located in the pharynx.
A taste bud that is located on the roof of the mouth.
A taste bud that is located in the esophagus.
The pharyngeal nerve (pterygopalatine nerve) is a small branch arising from the posterior part of the pterygopalatine ganglion. It passes through the pharyngeal canal with the pharyngeal branch of the maxillary artery, and is distributed to the mucous membrane of the nasal part of the pharynx, behind the auditory tube.
ganglionic branch of maxillary nerve to pterygopalatine ganglion
sensory root of pterygopalatine ganglion
A taste bud that is located on the skin of the trunk.
The artery of bulb of vestibule is a branch of the internal pudendal artery.
Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain.
olfactory tract linking bulb to ipsilateral dorsal telencephalon
A gland in the glandular region of the oviduct that secretes albumen over the ovum. In birds there are two regions of the oviduct, the first secretes a thin chalaziferous albumen layer, the second secretes a thicker albumen layer.
Subdivision of the head consisting of the area along the lower edge of the chin.
A collection of hairs that grows on the vertex (top of head).
The middle part of the head, located approximately equidistant from the left and the right sides of the head.
A longitudinal flap of skin that hangs beneath the lower jaw or neck.
A collection of hairs that grows on the external ear.
Subdivision of the head consisting of the area along the edge of the external ear.
A collection of hairs that grows on the forehead.
A bulge, knob, or swelling that protrudes from the forehead.
Subdivision of the head consisting of the left half of the face, vertically divided.
A ridge or peak located along the middle part of the head, located approximately equidistant from the left and the right sides of the head.
A benign tumor on the skin, usually with darker pigment.
An ectopic melanophore accumulation analogous to a nevi (mole) in humans.[TAO]
Anatomical structure consisting of either corner of the mouth.
Subdivision of the head consisting of the area along the front edge of the external nose.
The extreme point of curvature of the external nose.
Subdivision of the head consisting of the right half of the face, vertically divided.
A zone of skin that is part of the snout.
Subdivision of the head consisting of the pointed or rounded end or extremity of the snout.
Subdivision of the head consisting of the pointed or rounded end or extremity of the external ear.
in the FMA, vertex is a point and not a subdivision
A collection of hairs that grows on the snout.
A zone of skin that is part of the face.
A multilobulated modified sebaceous gland that is located at the base of the external ear, lined by stratified squamous epithelium, and secretes into the auditory canal
Zymbal's glands are located beneath squamous epithelium at the anterior and posterior aspect of the ear canal, and as a single external gland that is located anterior and ventral to the base of the external ear canal. The bilateral Zymbal’s glands are adjacent to the auditory canal and are made up of several lobules of modified sebaceous glands - http://ratguide.com/health/neoplasia/zymbals_gland_tumor.php.
located anterior and ventral to the exterior ear canal in rodents[MP:0013384]
The parenchyma of the spleen, consisting of lymphocytes and macrophages. It lies between the splenic trabecula. Red pulp is the part suffused with blood and white pulp consists of areas of lymphatic tissue where there are sleeves of lymphocytes and macrophages.
Enlarged and broad extension of the scapula distal to the glenoid region that conforms to the contour of the ribs. Origin for the major shoulder muscles including the deltoid group.
In non-tetrapod sarcopterygians the role of the scapula blade is filled by the enlarge cleithrum.
Anatomical space that contains a portion of the lateral line system.
TO DO: think about definitions for spaces in bone, in which pass through nerves, muscles, tendons and are defined by them.
Paired cartilaginous element forming the posterior portion of the pelvic girdle. [D.F. Markle, BULLETIN OF MARINE SCIENCE. 30(1): 45-53. 1980]
paired fin radial element that is composed of bone tissue.
The median, elongated basal cartilage of the pectoral fin.
Relevant for Elasmobranchii, Holocephali and primitive Teleostomi.
Pelvic fin radial that develops from the pelvic fin endoskeletal disc. Pelvic fin distal radials are paired.
Pelvic fin radial that is an endochondral fused radials or pterygiophores at the base of the pelvic fin.
Pelvic fin radial in the middle of the pelvic fin.
Radial element that is part of a paired fin.
Pelvic fin radial element that develops from the pelvic fin endoskeletal disc. Pelvic fin distal radial elements are paired.
Pelvic fin radial element that is an endochondral fused radial elements or pterygiophores at the base of the pelvic fin.
Obsoleted because basipterygium is not a type of radial.
obsolete pelvic fin basipterygial radial element
Pelvic fin radial element in the middle of the pelvic fin.
paired fin radial element that is composed of cartilage tissue.
The visible division between epiblast and hypoblast in the gastrula. Kimmel et al, 1995.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Small but distinctive epithelial sac containing fluid, located midventrally posterior to the yolk cell or its extension, and transiently present during most of the segmentation period. Kimmel et al, 1995. Kupffer's vesicle has been compared to the mouse embryonic node. Drummond et al, 2005.
TO DO: replaced by CL:0007016 not in release of CL yet.
The anterior round region of the yolk cell present after the yolk extension forms during the segmentation period. Kimmel et al, 1995.
A group of cells that migrate at the leading edge of shield during gastrulation but do not involute. At the end of gastrulation, forerunner cells migrate deep into the embryo and organize to form Kuppfer's vesicle. Cooper and D'Amico, 1996.
incorrectly generalized to teleosts so being obsoleted. 'embryonic structure' and develops_from some 'noninvoluting endocytic marginal cell cluster'
Surface structure that will develop into one of the median fins. Extends from dorsal surface of fish, caudal to the 8th somite, to the ventral surface ending at the caudal side of the vent.
Portion of the somite giving rise to body wall muscle masses. Kimmel et al, 1995.
Actinotrichium which is part of the dorsal fin fold.
The hatching gland rudiment at the time it underlies the forebrain during the early segmentation period. Kimmel et al, 1995.
removed axiom: part_of some 'sensory system'. Seems out of scope for uberon and/or not very useful as a class.
Undifferentiated mesodermal component of early trunk or tail segment or metamere, derived from paraxial mesoderm; forms the myotome, sclerotome and perhaps dermatome. Kimmel et al, 1995.
Actinotrichium which is part of the ventral fin fold.
Nutrient store for embryonic development in the form of semicrystalline phospholipoprotein and contained within yolk granules. Kimmel et al, 1995.
Peripheral layer of the yolk cell including nuclei and non-yolky cytoplasm. Kimmel et al, 1995.
Elastoidin fin ray that is slender, sometimes branched distally and present in the embryonic fin fold. Actinotrichia are translucent and exhibit birefringence.
Actinotrichia are required for lepidotrichium development. They are occasionally retained in adult fishes. Further taxon comments from Witten & Huysseune (2007): 'Actinotrichia are found in the embryonic fin fold, along the outer edge of the fin in Actinopterygii, and in the adipose fin in teleosts (Starck 1979; G�raudie and Meunier 1982; Becerra et al. 1983). Only in polypterids has their presence been reported in the joints between adjacent lepidotrichial elements (G�raudie 1988). In the sarcopterygian lineage, actinotrichia are present in coelacanths (G�raudie and Meunier 1980) and in young dipnoans (Arratia et al. 2001).'
Apical ectodermal ridge that is part of the dorsal fin.
A cell arising during cleavage; the term encompasses the partially cleaved, incomplete cells at the blastodisc margin before they collectively form the yolk syncytial layer (YSL) in the midblastula. Kimmel et al, 1995.
Term already present in CL. For the subclasses, see http://purl.obolibrary.org/obo/cl/tracker/18
Region of the median fin fold that develops into the dorsal fin.
Dermal bone that is located on the dorsal margin of the maxilla, usually at the dorso-posterior region of maxilla. The supramaxilla is a paired bone.
The supramaxilla may be present as one or two bones.
Dermal bone that is located dorsal to the preopercle or lies on the antero-dorsal corner of the opercle, and encloses the upper section of the preopercular canal. The suprapreopercle is paired.
Synonyms: supraopercle (Roberts 1969) supraopercular bone (Buckup 1998)
The posterior elongated region of the yolk cell that forms during the segmentation period. Kimmel et al, 1995.
Ganglion that develops from a cranial ectodermal placode and contains sensory neurons that innervate a lateral line.
Neuromast that is part of the mandibular lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
Dermal bone positioned as the first bone of the infraorbital series. The antorbital articulates with the lacrimal or infraorbital 1 anteroventrally and the supraorbital posterodorsally. The antorbital is a paired bone.
The antorbital in some teleosts fuses with the lacrimal. The antorbital contains the end branch of the infraorbital canal or neuromasts for the infraorbital canal in basal teleosts such as elopiformes, some osteoglossomorphs and fossil basal teleosts.
Neuromast that is part of the otic lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
Brightly refractile stone-like organ within the otic vesicle and positioned over a sensory macula; two form in each vesicle during the late segmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for otolith by T. Whitfield.)
Median fin skeleton that is located posterior to the anus.
Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)
Replacement bone that is bilaterally paired and articulates dorsally with the hyosymplectic cartilage or the articulation of the hyomandibula and symplectic.
It articulates ventrally with the posterior end of the posterior ceratohyal.
Cranial nerve which enters the brain between cranial nerves VIII and IX; contains afferents and sensory efferents to the posterior lateral line ganglion and middle ganglion. Fibers from the posterior lateral line ganglion innervate the occipital dorsal lateral line and trunk lateral lines.
posterior zone of dorsal telencephalic area
Part of the anterior commissure which abuts the preoptic region dorsally.
Replacement bone that is bilaterally paired and articulates with the anterior ceratohyal posteriorly and the ventral hypohyal bone ventrally.
removed axiom: part_of some habenula. Obsoleted because this term refererences a teleost specific region of the habenula, that has a homology relationship with a different portion of the habenula in mammals - that is currently not represented in Uberon. Can reinstate upon further classification of habenular structures.
A section of a pharyngeal arch artery that carries blood away from the gills.
efferent portion of pharyngeal arch artery
An endochondral bone which is located anterior to the orbitosphenoid and medial to the paired lateral ethmoid. Rhinosphenoid is a median bone.
gigantocellular part of magnocellular preoptic nucleus
Infraorbital that is the first (anteriormost) bone of the infraorbital series.
Suborbital and infraorbital 1 are synonymized by some authors (e.g., Cuvier), however, a suborbital bone in fishes has a different meaning than an infraorbital 1; it is a bone(s) that it is placed between the postero-dorsal infraorbitals and preopercle. A suborbital (also named postorbital by some authors) is not present in extant teleosts with the exception of Arapaima where it is occasionally present. Suborbital bones are found in some fossil basal teleosts. [G. Arratia]
Process that is the ventral, posteriorly-oriented bony extension of the quadrate.
Endochondral bone that separates the olfactory region from the orbit, extends medially to meet its fellow medially below the frontal bones and is bordered by the mesethmoid anteriorly. It may articulate with the autopalatine and infraorbital 1 laterally. The lateral ethmoid is paired.
Macula positioned on the floor of the utricle adjacent to the utriculosaccular foramen at the base of the common crus.
magnocellular superficial pretectal nucleus
olfactory tract linking bulb to ipsilateral ventral telencephalon
Endochondral bone that articulates laterally with the medial surface of the cleithrum and ventro-medially with the scapula and coracoid. Meoscoracoid bone is a small, arch-like bone that develops from the mesocoracoid cartilage. Mesocoracoid bone is paired.
Endochondral bone that forms the posteriormost element of the palatal complex. It overlies the quadrate and symplectic, posteriorly it articulates with the hyomandibula and anteriorly with the entopterygoid and ectopterygoid. It curves dorsally to form the posteroventral surface of the orbit. The metapterygoid is paired.
Dermal bone that forms the postero-dorsal part of the opercular series. The opercle articulates with the hyomandibula antero-dorsally and with the subopercle ventrally. The opercle is a paired bone.
The opercle is usually a large, flat bone that may be partially covered by the posterior region of the preopercle.
A fin that is fleshy, lacks supporting rays, and is located posterior to the dorsal fin.
One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)
Dermal bone that is part of the opercular series and bears the preopercular sensory canal. The preopercle is a paired bone and typically L-shaped, with the horizontal limb overlying the interopercle and the vertical limb overlying the opercle.
Portion of presumptive mesoderm fated to become dorsal mesoderm.
anal fin proximal radial element that is composed of bone tissue.
radial element that is composed of bone tissue.
Radials may be cartilaginous or bony; always present at the base of fins; typically support lepidotrichia.
rostrolateral thalamic nucleus of Butler & Saidel
secondary gustatory nucleus medulla oblongata
Specialized neuronal receptor cells of the lateral line and acoustico-vestibular systems. Kimmel et al, 1995. (Also see Anatomical Atlas entry for hair cells by T. Whitfield.)
Dermal bone that is part of the opercular series, lying below the opercle. The subopercle is paired and is typically a thin bone.
A dermal bone that is the lower, horizontal portion of the preopercle bone.
Lateral line sensory nucleus located in the cerebellum that processes sensory input from the lateral line.
obsolete ventral entopeduncular nucleus V
Replacement bone that is bilaterally paired and articulates with the ceratohyal bone posteriorly and the dorsal hypohyal bone dorsally.
The portion of the YSL that is outside of the blastoderm margin during epiboly. Kimmel et al, 1995.
CNS white matter that is part of the brain stem or spinal cord[ZFIN].
brain stem/spinal tracts and commissures
A dermal bone that is the upper, vertical portion of the preopercle bone.
Endochondral bone which is the posterodorsal region of the basioccipital bone.
dorsal zone of median tuberal portion of hypothalamus
Epipleurals lie below the horizontal septum and are posteroventrally directed. There are ossified epipleurals in certain ostariophysans. In many lower elopocephalan teleosts including ostariophysans the epipleural bones develop an anterodorsal branch so that they are forked proximally.
Dermal bone that is a projection present on the inner surface of a branchial arch.
Replacement bone that is bilaterally paired and articulates medially with a median skeletal element and laterally with a ceratobranchial cartilage or bone.
Laterally flattened haemal spine of an ural vertebra that lacks its arch and supports a few principal caudal lepidotrichia distally. A hypural may articulate or fuse with its ural centrum proximally or may lie ventral to the notochord. A hypural is an unpaired median bone that ossifies perichondrally. (Modified from Monod, 1968 and Arratia and Schultze, 1992).
interpeduncular nucleus medulla oblongata
Actinotrichium that is part of the dorsal fin skeleton.
Actinotrichium that is part of the anal fin skeleton.
Dermal bone that is located anterior, ventral or posterior to the eye. Infraorbital bones may or may not contain the infraorbital sensory canal. Infraorbital bones are numbered starting with the anteriormost element of the series.
Jaw muscle that connects the sphenotic to the metapterygoid and hyomandibula and promotes the elevation/abduction of the suspensorium.
medial funicular nucleus medulla oblongata
Multi-tissue structure which is part of the hypothalamus and consists of caudal and ventral zones, and is separated from the dorsal hypothalamic zone by a deep ventral sulcus. From Neuroanatomy of the Zebrafish Brain.
secondary gustatory nucleus trigeminal nuclei
TO DO: see DOI: 10.1002/cne.902660403 for next steps in defining different octaval nerve nuclei.
parvocellular superficial pretectal nucleus
periventricular nucleus of caudal tuberculum
Dermal bone placed postero-medially to the supracleithrum and/or cleithrum.
Commonly, the postcleithra form a bilateral series including one to three flat, thin postcleithra of variable shapes (in teleosts). Basal teleosts may have a series up to seven postcleithra (see Arratia 1984 and 1997 and references herein).
Endochondral bone that sutures with the orbitosphenoid anteriorly, the frontal bone dorsally and the sphenotic and prootic posteriorly. The pterosphenoid forms part of the orbitosphenoid region. The pterosphenoid bears foramina that accommodate branches of the trigeminal and facial nerves. The pterosphenoid is a paired bone.
The retroarticular is a cartilage bone that forms at the posteroventral tip of Meckel's cartilage where the interoperculomandibular ligament attaches (5.1 mm NL). In the adult it is basically triangular in shape. The retroarticular is ligamentously connected to the interopercle and preopercle posteriorly and abuts the ventral shelf of the dentary anteriorly.
Cranial nerve which enters the brain between cranial nerves VI and VII; contains afferents and sensory efferents to the anterior lateral line ganglia.
Neural arch and Weberian ossicle that is reduced in size relative to other neural arches. Scaphium has a process which articulates with the first centrum.
Actinotrichium that is part of the caudal fin skeleton.
Haemal spine of last hemal arch that is pierced by the haemal canal through which the caudal vessels pass or haemal arch of preural centrum 1. Its distal part commonly supports lepidotrichia. The parhypural is an unpaired median haemal spine.
The parhypural is frequently confused with the arch plus spine of preural centrum 1.
Endochondral bone that is median and located in the dorsal skeletogenous septum between the cranium and the dorsal fin.
Tendon bone that forms in the tendon of the sternohyoid muscles ventral to the anterior end of copula 1. The urohyal associates by ligaments to the ventral hypohyals or it articulates with the ventral hypohyals. The urohyal is an unpaired bone.
The urohyal forms as a single ossification in most teleosts, or as a paired ossification.
Actinotrichium that is part of the adipose fin.
Bone that is an element associated with a Weberian vertebra.
Small membrane bone homologous with a cartilage bone in more basal fishes (Patterson, 1977). Situated between the exoccipital and the pterotic at point of attachment of short ligament that originates on the ventral arm of the posttemporal.
Dermal bone that is a flattened element that supports the branchiostegal membrane. Branchiostegal rays are generally present in a series articulating ventrally or ventro-medially with the anterior and posterior ceratobranchials whereas the most posterior ray articulates with the subopercle. The branchiostegal ray is paired.
Although the branchiostegals are articulated or attached to the hyoid arch, they belong to the opercular series. Branchiostegal rays are of variable shape and number and their homology is problematic. Usually they are numbered from anterior to posterior elements, instead from posterior to anteriorly considering that the last element of the series is consistently associated to the subopercle. For a survey of branchiostegal rays see Mc Allister (1968).
Hindbrain nucleus which is part of the medulla oblongata and is a mechanoreceptive area along with the medial octavolateralis nucleus. It is smaller than the medial octavolateralis nucleus and is located lateral to the facial and vagal lobes of the medulla oblongata. From Neuroanatomy of the Zebrafish Brain.
Endochondral bone that is bilaterally paired and forms part of the ventral branchial arches.
Infraorbital that is the fifth bone of the infraorbital series.
Some or all epineural bones ossify free from the neural arches in most teleosts. In some lower teleosts, e.g., Leptolepis, Hiodon, elopiforms and albuliforms, ossification proceeds from the attachment point of the ligament to the arch, and the epineural is a process of the neural arch. In many lower teleosts epineurals are forked proximally.
pelvic fin radial element that is composed of bone tissue.
Neural arch and Weberian ossicle that has been modified in shape relative to other neural arches. Intercalarium includes three parts: an anterolateral process (the manubrium) which is embedded in the interossicular ligament and the ascending and articulating processes.
Axial bone which is a segmental ossification that forms in the myoseptum.
Intermuscular bones are found in teleosts fishes only.
Endochondral bone of the branchial arches located medial to the epibranchials.
Cells (incompletely cleaved before the YSL forms), located at the surface just at the rim of the blastodisc, external to the deep blastomeres. Kimmel et al, 1995.
Actinotrichium that is part of the pectoral fin.
Dermal bone of the secondary pectoral girdle that attaches the girdle to the skull. Its dorsal process attaches to the epiotic or epioccipital, the ventral process to the intercalar and the body articulates with the supracleithrum. The postotic sensory canal or lateral line runs within or lateral to bone.
The posttemporal is commonly a Y-shaped bone with two elongate processes. The dorsal process may be equal or longer than the ventral process or the opposite. The ventral process may be absent in some teleosts.
Last caudal vertebra identified as the point at which the caudal vessels bifurcate, leaving the protection of the haemal arches of the caudal vertebrae and running laterally to the hypurals. This vertebra bears, commonly, a well-developed haemal arch and its spine (parhypural).
The haemal arch may be fused to the centrum or not. In contrast, the neural arch and spine may be well developed, or rudimentary or absent in different teleost subgroups.
Endochondral bone that articulates with the autosphenotic anteriorly, the parietal dorsomedially, the prootic ventrally (and the intercalar occasionally), and the epiotic and exoccipital posteriorly. The pterotic encloses the horizontal semicircular canal of the inner ear. The lower edge of the pterotic contributes to the hyomandibular facet. The pterotic is paired.
Cranial cartilage which is a small median cartilage located between the premaxillae and anterodorsal to the ethmoid.
Vertebra anterior to preural centrum 1; sometimes termed the 'antepenultimate' vertebra. Mabee and Bird, 2001.
Endochondral bone that sutures with the pterosphenoid anteriorly, the prootic ventrally, the frontal bone dorso-medially, and the pterotic dorso-posteriorly. Occasionally the sphenotic sutures with the parietal bone. The sphenotic separates the orbital from the otic region. The sphenotic bears a large antero-lateral or lateral or ventro-lateral process that borders the postero-dorsal margin of the orbit. The sphenotic is a paired bone.
The lower edge of the sphenotic may contribute to the hyomandibular facet depending on the fish group.
superior reticular formation medial column
Dermal bone that articulates dorsally with the posttemporal and ventrally with the cleithrum. Supracleithrum is part of the secondary pectoral girdle and commonly, carries part of the lateral line canal.
The dorsalmost postcleithrum or postcleithrum 1 may lie medial to the ventral part of the supracleithrum. The postotic canal or lateral line may run close to the dorsal margin or in the upper third or in the lowest third of the bone depending on the fish group.
Actinotrichium that is part of the pelvic fin.
Neural arch that extends along the dorso-lateral surface of the last preural centra and/or ural centra and the notochord (Arratia & Schultze, 1992). An uroneural develops as a modification of the neural arch of an ural centrum (Patterson, 1968). The series of uroneurals may include from 7 to 1 elements that are numbered from rostrad to caudad. An uroneural is a paired membrane bone.
The presence of modified ural neural arches or uroneurals is interpreted as a synapomorphy of Teleostei. Uroneurals present some modifications in certain teleost subgroups and such specialized structures are named pleurostyle (e.g., ostarioclupeomorphs) and stegural (e.g., salmonids).
removed axiom: part_of some 'pharyngeal muscle' no information about this class, may be zebrafish specific nomenclature.
obsolete ventral oblique branchial muscle
ventral rhombencephalic commissure brain stem
Connective tissue partitions developing between the myotomes. Kimmel et al, 1995.
A brainstem commissure that contains major crossed descending projections from both tectal lobes.
This class is present in fishes and amphibians.
Endochondral bone that is part of the antero-lateral region of the palate. Commonly, it articulates with the maxilla anterolaterally and with the ethmoidal region medially. It may also articulate with the dermopalatine ventro-laterally and with the entopterygoid posteriorly. The autopalatine is paired.
The cartilaginous autopalatine forms from the anterior palatoquadrate arch. Possession of a dorsomedial process, which abuts the ethmoid, is a unique feature shared by Cypriniformes (Fink and Fink, 1981). The palatine has two components, the autopalatine (derived from pars autopalatine) and the dermal component having teeth, the dermopalatine Arratia & Schultze 1990. The element in cypriniforms is only the cartilage part, so that it is more correct to name it autopalatine and not as palatine in general that it implies a fusion of elements (as in perciforms).
Surface structure which is a tactile structure found in the branchial region. Barbels are covered with epidermis rich in taste buds, and are innervated by branches of the cranial nerves.
basipterygium element that is composed of bone tissue.
Replacement bone that is bilaterally paired and articulates anteriorly with the anterior ceratohyal.
Posterohyal is used in Rapp Py Daniel (1997).
Caudal part of the abducens nucleus that mediates motor function.
caudal zone of median tuberal portion of hypothalamus
Postcranial axial cartilage and Weberian ossicle that is located dorsal to the scaphium. The claustrum cartilage is bilaterally paired.
Part of the anterior commissure which is located immediately ventral to the supracommissural nucleus of area ventralis telencephali.
commissure of the secondary gustatory nuclei
decussation of the medial octavolateralis nucleus
obsoleted because was artificially generalized from zebrafish, wherein it is currently obsolete.
anal fin distal radial element that is composed of bone tissue.
Musculature that is part of the dorsal fin.
Rostral part of the abducens nucleus that mediates motor function.
removed axiom: white matter and part_of some 'optic tract'. Not clear that directional labels for optic tract parts are consistent across taxa. To be reviewed.
Dermal bone that forms the ventro-medial part of the palate and the antero-ventral and ventral wall of the orbit. The entopterygoid is a paired bone.
Dorsal branchial arch bone that is bilaterally paired and articulates laterally with ceratobranchial cartilage or bone and medially with pharyngobranchial cartilage or bone.
A free, modified neural spine of a preural or a ural vertebra that is placed between the last developed neural spine of a preural centrum and the dorsal axis (= anterior margin of first uroneural) of the caudal skeleton . An epural commonly supports one or more dorsal procurrent rays. An epural is an unpaired median perichondrally ossified bone.
The origin of the epurals is unclear, three hypotheses have been proposed: 1) The epurals are modified radials or dorsal radials; 2) the epurals are detached neural spines and may support fin rays; and 3) the epurals are a serial homologue of the supraneuralia. At least in teleosts the epural is a detached neural spine. For details see Schultze and Arratia (1989) and Arratia and Schultze (1992).
Dermal canal-bearing bone placed at the dorso-posterior region of the skull roof, lying on the posterior region of the pterotic and parietals, or the pterotic and epioccipital, or on the pterotic, epioccipital and occipital bones.
When it is present, the paired series of extrascapular bones may include one pair or two pairs or two pairs plus a median one. The most lateral is named lateral extrascapula and is the bone where the intersection of the otic, postotic and extrascapular or supratemporal canals occur. The medial and median extrascapulars carry the extrascapular or supratemporal canal.
A pair of HA are connect one to each AA1. They run rostromedially until at the extreme rostro-ventral midline the two vessels merge and then run straight caudally along the ventral midline until they reach the cranial end of the ventral aorta (VA). There, the single HA passes just dorsal to the rostral end of the VA and then immediately splits again into a pair of HA. The paired HA continue caudally just to either side of the ventral midline. The HA provide blood supply to the ventral branchial region and the heart.sogai et al. 2001.
Dermal bone that is part of the opercular series. It is located ventro-medially to the preopercle and anterior to the subopercle. It is joined to the posterior part of the lower jaw (retroarticular) by a ligament. The interopercle is paired.
Dermal bone that is part of the dorsal or upper border or antero-dorsal border of the orbit. The supraorbital bone may contact the orbital margin of the frontal bone medially, the antorbital antero-ventrally and the dermosphenotic posteriorly. The supraorbital bone does not carry sensory canals. The supraorbital bone is paired.
The supraorbital bone may be present as two or one bone in extant teleosts, although many of the advanced forms lack the bone.
Replacement bone that is bilaterally paired and articulates with the hyomandibula and the quadrate.
When the interhyal bone or cartilage is present it articulates at the articulation of the hyomandibula and symplectic.
Tooth that forms on ceratobranchial 5 cartilage or bone.
Ceratobranchial 5 teeth are the only teeth present in zebrafish and other cypriniforms.
Endochondral bone, membrane bone, and Weberian ossicle that is an element of third vertebra. Anteriorly it attaches to the interosseus ligament and posteriorly it extends as a transformator process embedded in the tunica externa of the swimbladder.
Process that is the dorsally directed, vertical process of the entopterygoid. The strut sometimes articulates with the orbitosphenoid.
Fink and Fink 1981, present in gymnotoids.
removed axiom: part_of some 'optic tract' Not clear that directional labels for optic tract parts are consistent across taxa. To be reviewed.
viscerosensory commissural nucleus of Cajal
A multilayer of deep cells of fairly uniform thickness that forms during early epiboly (at dome stage; upon conversion of the blastodisc to the blastoderm); during gastrulation the DEL (deep cell layer) gives rise to the epiblast and hypoblast. Kimmel et al, 1995.
The portion of the YSL that lies deep to the blastoderm during epiboly. Kimmel et al, 1995.
A section of a pharyngeal arch artery that delivers blood to the gills.
Artery that is part of the pharyngeal arches 3-5, and forms the afferent portion of a loop off of the aortic arch[ZFA].
afferent portion of pharyngeal arch artery
Apical ectodermal ridge that is part of the median fin fold.
Somite-derived body wall muscle present dorsal to the horizontal myoseptum. Kimmel et al, 1995.
Caudal vertebra that is one of the last caudal vertebrae anterior to the ural vertebrae that with its neural and haemal spines supports the procurrent caudal fin rays or lepidotrichia. The numbering of preural vertebrae is from caudal to rostral direction.
The term preural vertebra was created by Nybelin (1963) for those vertebrae supporting caudal procurrent rays. For additional information see Arratia and Schultze (1992). Their neural and hemal arches may or may not be fused to their corresponding autocentrum. Fusion or separation of certain neural and/or haemal arches of preural centra is characteristic or certain teleosts subgroup. The boundary between preural and ural region is determined by the bifurcation of the four or five blood vessels running inside the hemal arches of the preural vertebrae (primary caudal artery, two secondary arterial trunks, primary caudal vein, and secondary subvertebral vein) (for details see Schultze & Arratia, 1989). The bifurcation of the caudal artery and vein was proposed as a landmark to homologize preural centrum 1 throughout actinopterygians (Nybelin, 1963).
Paired, ventromedially directed processes on the posterior ends of the centra, ligamentously joined to the hemal postzygapophyses of the immediately posterior vertebra. The most posterior caudal vertebrae lack hemal postzygapophyses.
Somite-derived body wall muscle present ventral to the horizontal myoseptum. Kimmel et al, 1995.
Neuromast that is part of the infraorbital lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
Neuromast that is part of the opercular lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
nucleus of the medial longitudinal fasciculus medulla oblongata
nucleus of medial longitudinal fasciculus of medulla
obsolete postcommissural nucleus of V central entopeduncular nucleus
Medial ventral region of the somite that will form vertebral cartilages. Kimmel et al, 1995.
Median fin skeleton supporting the caudal fin.
Somite-derived body wall muscle present dorsal to the horizontal myoseptum. immel et al, 1995.
Endochondral bone that is the anterodorsally oriented process of the third neural arch.
transverse process of the third vertebra
Portion of the somite giving rise to body wall muscle masses. Kimmel et al, 1995.>
dorsal fin distal radial element that is composed of bone tissue.
Neuromast that is part of the middle lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
Neuromast that is part of the posterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
nucleus of the medial longitudinal fasciculus synencephalon
dorsal fin proximal radial element that is composed of bone tissue.
Medial ventral region of the somite that will form vertebral cartilages. immel et al, 1995.
ventral rhombencephalic commissure medulla oblongata
medial funicular nucleus trigeminal nuclei
removed axiom: part_of some 'central nervous system' Seems out of scope for uberon and/or not very useful as a class.
Portion of the somite giving rise to body wall muscle masses. immel et al, 1995.
A neuromast that is part of the occipital lateral line.
A neuromast that is part of the supraorbital lateral line.
Lateral process, spine-like or crest-like, at the lateral wall of the haemal arch of the parhypural that serves for insertion of the hypochordal longitudinal muscle. The process may contribute to the lateral protection of the parhypural foramen (where the caudal blood vessels exit the hemal arch) and the hypural foramen (where a caudal heart may be present). The hypurapophysis is paired.
The structure, the processus parhypurale, was given the name of hypurapophysis by Nursall (1963). Additional processes may be present on the lateral walls of hypurals 1 and 2 in some teleost subgroups. They are named primary, secondary hypurapophyses, etc.
caudal division of the internal carotid artery
The paired vessels that run along the lateral walls of the hindbrain and drain into the anterior cardinal veins. Isogai et al. (2002)
Connect the outflow of the aortic arches to the dorsal aorta. The place where the lateral dorsal aorta fuse is is called the radiax of the aorta. Isogai et al. 2001.
The caudal fin is the most posterior median fin. It is composed of a complex of three modified centra and modified neural and hemal arches and spines. Mabee and Bird, 2001.
rostral division of the internal carotid artery
cranial division of the internal carotid artery
Basidorsals are bilaterally paired cartilages on the dorsolateral side of the notochord which are replaced by ossified neural arches or dorsal arcocentra. In otophysan fishes, basidorsal 1, bd2, bd3, and bd4 give rise to parts of the Weberian apparatus.
Branches dorsally from the cranial division of the internal carotid artery, then curves caudally along the dorsal medial wall of the eye capsule to drain into the PMBC just rostral to the midbrain hindbrain boundar[ZFIN:curator]y
This anteriormost portion of the intestine has the most digestive enzymes and the greatest epithelial surface area. Wallace et al, 2005.
this class and all children are being obsoleted from uberon because they were unnecessarily generalized into TAO and because they are cell types.
Annotation with this anatomy term indicates that a structure was not specified by the author.
An otic sensory epithelium that will develop into the mature macula.
immature sensory hair cells anterior macula
obsolete immature hair cell anterior macula
immature sensory hair cells posterior macula
obsolete immature hair cell posterior macula
A protuberance in front of the gential pore and behind the vent. Mature females have a well developed urogenital papillae whilst in mature males it is poorly developed. Brion et al, 2004.
Median fin skeleton located on the dorsal surface of the organism.
The dorsal marginal region of the YSL where maternal dorsal determinants localize. Participates in positioning the shield. Ho et al, 1999.
The NEM cell cluster lies in a superficial position of the dorsal blastoderm margin encompassing EVL cells and one or two layers of underlying deep cells. Unlike other marginal blastomeres, cells in this cluster do not participate in involution. Cooper et al, 1996.
noninvoluting endocytic marginal cell cluster
Tooth row that is the ventralmost row of teeth on ceratobranchial 5 bone.
Tooth row that is the mediodorsal row of teeth on ceratobranchial 5 bone, located between the dorsal tooth row and ventral tooth row.
Tooth row that is the dorsalmost row of teeth on ceratobranchial 5 bone.
Ceratobranchial 5 tooth which is the anteriormost tooth in the ventral tooth row.
Ceratobranchial 5 tooth which is the posteriormost tooth in the ventral tooth row.
Ceratobranchial 5 tooth which is posterior to tooth 3V and anterior to tooth 5V in the ventral tooth row.
Ceratobranchial 5 tooth which is posterior to tooth 1V and anterior to tooth 3V in the ventral tooth row.
Ceratobranchial 5 tooth which is posterior to tooth 2V and anterior to tooth 4V in the ventral tooth row.
Ceratobranchial 5 tooth which is the anteriormost tooth in the mediodorsal tooth row.
Ceratobranchial 5 tooth which is posterior to tooth 1MD and anterior to tooth 3MD in the mediodorsal tooth row.
Ceratobranchial 5 tooth which is the anteriormost tooth in the dorsal tooth row.
Ceratobranchial 5 tooth which is the posteriormost tooth in the dorsal tooth row.
Ceratobranchial 5 tooth which is the posteriormost tooth in the mediodorsal tooth row.
Ceratobranchial 5 tooth which is posterior to tooth 2MD and anterior to tooth 4MD in the mediodorsal tooth row.
A migrating group of cells originating from the posterior lateral line placode. The primordium deposits seven to nine neuromasts and interneuromasts between them during its posterior migration to the tail. Gompel et al, 2001.
Scute that is a bony plate that forms in dorsal midline of body margin between the skull and dorsal fin.
Median fin that is located posterior to the anus.
Vertebra that is posteriorly adjacent to vertebra 1.
Vertebra that is posteriorly adjacent to vertebra 2.
Vertebra that is posteriorly adjacent to vertebra 5.
Endochondral bone and Weberian ossicle that is an element of the fourth vertebra that curves ventrally around the anterior head of the swim bladder.
Cartilaginous larval structure dorsal to the four anterior-most vertebrae, which forms the connection between neural arches and supraneurals in the Weberian apparatus. Bird and Mabee, 2003.
A layer of collagen fibrils present in the imature integument in an acellular subepidermal space. At first, the fibrils are all oriented in the same direction, later they form the complex plywood-like structure that is characteristic of the dermal deep region. Le Guellec et al, 2004.
Anatomical cluster that consists of the anteriormost vertebrae and associated structures that connect the swim bladder to the inner ear.
Vertebra 1-4, and sometimes vertebra 5 in some catfishes, are part of the Weberian apparatus. Weberian apparatus is present in Otophysi.
Vertebra that is part of the Weberian apparatus.
Weberian vertebra are usually vertebra 1-4. Present in Otophysi.
Supraneural bone located dorsal to vertebra 2.
In otophysans, supraneural 2 bone is part of the neural complex.
Supraneural bone that is located dorsal to vertebrae 3 and 4.
In otophysans, supraneural 3 bone is part of the neural complex and fuses in development with neural arches 3 and 4.
Islands of eosinic cells found on the lateroventral surface of the kidney. Function is thought to be that of the parathyroid gland in other vertebrates, which are lacking in fishes. These cells secrete hypocalcin (teleocalcin) to regulate calcium metabolism.
Pharyngeal arch cartilage that is ventral, median, and associated with more than one pharyngeal arch in the pharyngeal arch 3-7 skeleton.
Copula that is ventral, median, and associated with pharyngeal arches 3-5.
Copula that is ventral, median, and associated with branchial arches 4 and 5 (pharyngeal arches 6-7).
Basibranchial bone that is ventral, median, and associated with branchial arch 1 (pharyngeal arch 3). Typically develops in the anterior copula cartilage.
Basibranchial bone that is ventral, median, and associated with branchial arch 2 (pharyngeal arch 4). Typically develops in the anterior copula cartilage.
Basibranchial bone that is ventral, median, and associated with branchial arch 3 (pharyngeal arch 5). Typically develops in the anterior copula cartilage.
Basibranchial bone that is ventral, median, and associated with branchial arch 4 (pharyngeal arch 6). Develops in posterior copula cartilage or basibranchial 4 cartilage.
Hypobranchial bone that is bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 1 element laterally. Develops in hypobranchial 1 cartilage.
Hypobranchial bone that is bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 4 element laterally. Develops in hypobranchial 4 cartilage.
Hypobranchial bone that is bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 3 element laterally. Develops in hypobranchial 3 cartilage.
Hypobranchial bone that is bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 2 element laterally. Develops in hypobranchial 2 cartilage.
Ceratobranchial bone that is bilaterally paired and articulates laterally with epibranchial 1 cartilage or bone.
Ceratobranchial bone that is the most posterior, bilaterally paired ventral pharyngeal arch bone.
Synonym 'lower pharyngeal' from Weitzman, 1962. Synonym 'inferior pharyngeal bone' from Saxena, S.C. (1960). The cranial musculature of a hill-stream cyprinid fish Garra mullya (Sykes). Proceedings of the National Institute of Science in India. 26B(4): 176-188. Synonym 'pharyngeal arch' from Eastman, J.T. (1971). The pharyngeal bone musculature of the carp, Cyprinus carpio. Journal of Morphology. 134(2): 131-140.
Ceratobranchial bone that is bilaterally paired and articulates laterally with epibranchial 4 cartilage or bone.
Ceratobranchial bone that is bilaterally paired and articulates laterally with epibranchial 3 cartilage or bone.
Ceratobranchial bone that is bilaterally paired and articulates laterally with epibranchial 2 cartilage or bone.
Epibranchial bone that is bilaterally paired and articulates laterally with ceratobranchial 1 cartilage or bone and medially with pharyngobranchial cartilage or bone.
Epibranchial cartilage that is bilaterally paired and located at the articulation of epibranchial 4 cartilage or bone and the posterior tip of ceratobranchial 4 cartilage or bone.
Epibranchial bone that is bilaterally paired and articulates laterally with ceratobranchial 4 cartilage or bone and medially with pharyngobranchial cartilage or bone.
Epibranchial bone that is bilaterally paired and articulates laterally with ceratobranchial 2 cartilage or bone and medially with pharyngobranchial cartilage or bone.
Epibranchial bone that is bilaterally paired and articulates laterally with ceratobranchial 3 cartilage or bone and medially with pharyngobranchial cartilage or bone.
Pharyngobranchial bone, located medial to the epibranchials and posteriorly adjacent to pharyngobranchial 1 element.
Most posterior pharyngobranchial cartilage, located medial to the epibranchials.
Pharyngobranchial bone, located medial to the epibranchials and posteriorly adjacent to pharyngobranchial 2 element.
Neural arch that is the second after the neurocranium.
The medial portion of the spinal cord floor plate, located adjacent to the notochord.
This class was obsoleted as it was discovered to be equivalent to an existing class
Stage I follicles (less than 140 microns) are primary growth stage. Selman et al, 1993.
Stage II follicles (140-340 microns) are cortical alveolus stage. Selman et al, 1993.
Stage III (340-690 microns) are vitellogenesis. Selman et al, 1993.
Fin or limb undergoing the process of regeneration.
Tendon bone located on the median side of the lower jaw, dorsal to Meckel's cartilage and medial to the angular. The coronomeckelian forms as an ossification of the tendon of the adductor mandibulae muscle. The coronomeckelian is a paired bone.
Endochondral bone that is the median element of the ventral hyoid arch, generally lying between the paired ventral hypohyals.
The anterior compartment of the swim bladder is thought to have acoustic resonance properties that play a key role in audition. It is connected to the posterior chamber via the dusctus communicans. Finney et al, 2006.
The posterior compartment of the swim bladder plays a key role in buoyancy control. It is connected to the anterior chamber via the dusctus communicans. Finney et al, 2006.
Branchiostegal ray that is the anterior-most ray in the adult.
Branchiostegal ray that is the third anterior-most ray in the adult.
Branchiostegal ray that is the second anterior-most ray in the adult.
The posterior lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the posterior lateral line system.
Dorsolateral placode that gives rise to the anterior lateral line.
Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS].
A tract originating in the epiphysis and fasiculating with the tract of the postoptic commissure. Ross et al, 1992.
Sublingual that is the single element resulting from the fusion of the sublingual dorsal ossification and sublingual ventral ossification.
Supradorsals are small paired nodules of cartilage positioned at the distal ends of neural arches and the proximal end of neural spines (Arratia et al., 2001).
Telencephalic nucleus containing the cell bodies of neurons whose axons form the anterior commissure.
obsolete nucleus of the tract of the anterior commissure
The nucleus containing the cell bodies of neurons whose axons form the postoptic commissure.
nucleus of the tract of the postoptic commissure
A zone of delayed differentiation at the midbrainhindbrain boundary. The IZ separates midbrain from anterior hindbrain neuronal clusters and has been described in all vertebrates. Geling et al, 2003.
stratum fibrosum et griseum superficiale
An unpaired left-sided accessory organ which plays a role in establishing lateral brain left right asymmetry. Gamse et al, 2003.
Basiventrals are bilaterally paired cartilages lateral to the notochord which are replaced by ossified parapophyses or hemal arches.
Anatomical cluster that consists of supraneural 2 bone and supraneural 3 bone and their extensions, and which is part of the Weberian apparatus.
Hemal spines are extensions of hemal arches in the ventral skeletogenous septum of the caudal region.
Cells that initially are located adjacent to the spinal cord and notochord along that migrate from their initial medial position radially through the myotome to the lateral surface of the somites.
likely very zebrafish specific so being obsoleted for now.
obsolete migratory slow muscle precursor cell
Epibranchials 1-3 in adults are compound elements formed by the fusion of epibranchial cartilages and the so-called uncinate processes. Posteromedially directed uncinate processes develop on the posterior edge of epibranchials 1-3. These appear as separate centers of chondrification (6.2 mm) that later fuse laterally to the posterior edges of the epibranchial cartilages (6.8 mm).
A epithelial-mesenchymal boundary that is part of a regenerating fin/limb.
epithelial mesenchymal boundary of regenerating fin/limb
A epithelium that is part of a regenerating fin/limb.
The anteror lateral line ganglia develops from cranial ectodermal placodes and contain sensory neurons that innervate the anterior lateral line system.
Parapophysis that is the lateral projections from the first centrum in cyprinids, absent in catostomids, and absent in characiphysans (Fink and Fink, 1996).
Parapophysis that is lateral projection from the second centrum, absent in Siluriformes (Fink and Fink, 1996).
Neural arch 3 is expanded and fused to supraneural 3 as part of a neural complex roofing and protecting the neural canal.
Neural arch 4 is expanded and fused to supraneural 3 as part of the neural complex. A reduced neural spine projects from the posterior margin of the neural complex.
The parapophysis + rib, fused to the centrum, extends laterally then angles anteroventrally. A thin plate, the os suspensorium fuses to its median surface.
Posterior to the Weberian apparatus, otophysan supraneurals form as median, unpaired, rod- or platelike elements, as in other actinopterygians.
Dermal bone that first appears as paired ossifications in the membrane (dermis) dorsolateral to the ethmoid cartilage and anterolateral to the lateral ethmoids, later having the appearance of one butterfly-shaped element. Fused to the anterodorsal margin of the mesethmoid. Bordered anteriorly by the kinethmoid and posteriorly by the frontal.
Small rounded to egg-shaped cartilage bone that sits in an anterolateral depression on the prevomer. Articulates with the autopalatine in all cypriniforms.
Sesamoid bone located in the premaxillary-ethmoid ligament, between the mesethmoid and the premaxilla. The kinethmoid is an unpaired median bone.
The kinethmoid is part of the protrusion mechanism of the upper jaw and is restricted to cypriniform fishes.
Infraorbital that is the second bone of the infraorbital series.
Infraorbital that is the third bone of the infraorbital series.
Infraorbital that is the fourth bone of the infraorbital series.
Endochondral bone that borders that medial edge of the posttemporal fossa. The epiotics are sutured to parietals and supraoccipital dorsally, the exoccipitals ventrally and the pterotics laterally. The epiotic is a paired bone.
pelvic fin distal radial 2 element that is composed of bone tissue.
pelvic fin distal radial 3 element that is composed of bone tissue.
pelvic fin distal radial 1 element that is composed of bone tissue.
Lepidotrichium which is part of the dorsal fin.
A range of seven to nine rod-like internal median skeletal support structures of the dorsal fin, comprised of both bone and cartilage and found between vertebrae 11 and 18.
A range of twelve to fourteen rod-like internal median skeletal support structures of the anal fin, comprised of both bone and cartilage and found between vertebrae 14 and 21.
Lepidotrichium which is part of the anal fin.
A duct connecting the esophagus to the posterior chamber of the swim bladder. Finney et al, 2006.
Sclerotic bone that is located anterior to the eye.
Sclerotic bone that is located posterior to the eye.
The constriction between the anterior and posterior chambers of the swim bladder. There does not appear to be an identifiable sphincter in the ductus, and therefore other musculature may regulate its opening. Finney et al, 2006.
Apical ectodermal ridge that is part of the pelvic fin.
A plate-like chondrogenic condensation within the pectoral fin, which subdivides into individual radials by decomposition of extracellular matrix in the inter-radial mesenchyme (Grandel and Schulte-Merker, 1998).
Cartilage which is part of the axial skeleton.
The anterior lateral line system develops from cranial ectodermal placodes, situated between the eye and the ear, that give rise to both the neuromasts and the anterior lateral line sensory nerves that innervate the neuromasts. The anterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians and are innervated by several lateral line nerves, which project to the hindbrain. The anterior lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.
The anterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The anterior lateral line develops from cranial ectodermal placodes situated between the eye and ear.
The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.
Neuromast that is part of the anterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
Cells (completely cleaved), located underneath the superficial blastomeres and internal to the marginal blastomeres. Kimmel et al, 1995.
Anatomical cluster consisting of the paired sublingual dorsal ossification and sublingual ventral ossification.
Sublingual that is the dorsal element paired with the sublingual ventral ossification.
Sublingual that is the ventral element paired with the sublingual dorsal ossification.
Nerve fibers originating from the dorsal anterior lateral line ganglion. These rami innervate the otic, supraorbital, and infraorbital neuromasts.
Nerve fibers originating from the ventral anterior lateral line ganglion. These rami innervate the mandibular and opercular neuromasts.
Nerve fibers originating from the middle lateral line ganglion. These fibers innervate the middle lateral line.
The middle lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the middle lateral line.
Cells (completely cleaved), located at the surface of the blastodisc, above the deep blastomeres. Kimmel et al, 1995.
Bilaterally paired medial bar of cartilage formed at midorbit through medial chondrification from triangles of cartilage that later form the junction of the taeniae marginales anterior, taeniae marginales posterior and the epiphyseal bar.
Cranial cartilage which is a paired anterodorsal projection of the posterior end of the parachordal cartilage. It lies lateral to the notochord, just anterior to the posterior tip of the otic capsule. The bilaterally paired occipital arch cartilages fuse anterodorsally to the posterior edges of the auditory capsules and meet medially as the tectum synoticum (by 12 dpf).
Cartilage bar (bilaterally paired) that grows anteroventrally from the epiphyseal bar to join the anterolatera1 edge of the ethmoid plate.
Cartilage formed via medial fusion between bilaterally paired trabecula crani.
Pharyngeal arch cartilage that is bilaterally paired and articulates dorsally with the hyosymplectic cartilage or the articulation of the hyomandibula and symplectic.
It articulates ventrally with the posterior end of the ceratohyal cartilage or the posterior ceratohyal.
Cartilage bar (bilaterally paired) that is first visible as an anterior extension of the auditory capsule. It grows anteriorly toward the middle of the orbit where it is connected to its mate on the other side by the epiphyseal bar.
Pharyngeal arch cartilage that forms the largest skeletal element of the ventral branchial arches.
Ceratobranchial cartilage that is bilaterally paired and articulates laterally with epibranchial 2 cartilage or bone.
Ceratobranchial cartilage that is bilaterally paired and articulates laterally with epibranchial 3 cartilage or bone.
Ceratobranchial cartilage that is bilaterally paired and articulates laterally with epibranchial 4 cartilage or bone.
Ceratobranchial cartilage that is bilaterally paired and articulates laterally with epibranchial 1 cartilage or bone.
Ceratobranchial cartilage that is the most posterior, bilaterally paired ventral pharyngeal arch cartilage.
Pharyngeal arch cartilage that is bilaterally paired and articulates medially with a median skeletal element and laterally with a ceratobranchial cartilage or bone.
The hypobranchial cartilage usually articulates medially with a basibranchial bone or cartilage.
Hypobranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 4 cartilage or bone.
Hypobranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 1 cartilage or bone.
Hypobranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 2 cartilage or bone.
Hypobranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 3 cartilage or bone.
Pharyngeal arch cartilage that is bilaterally paired and articulates laterally with ceratobranchial cartilage or bone.
Epibranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 1 cartilage or bone.
Epibranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 3 cartilage or bone.
Epibranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 2 cartilage or bone.
Epibranchial cartilage that is bilaterally paired and articulates laterally with ceratobranchial 4 cartilage or bone.
Sublingual cartilage that is the dorsal element paired with the sublingual ventral cartilage.
Paired cartilages that project medially from the medial tips of epibranchials.
Pharyngobranchial cartilage, located medial to the epibranchials and posteriorly adjacent to pharyngobranchial 2 element.
Pharyngobranchial cartilage, located medial to the epibranchials and posteriorly adjacent to pharyngobranchial 1 element.
Pectoral fin cartilage that is part of the embryonic primary pectoral girdle from which the mesocoracoid bone will ossify endochondrally.
Small cartilage that forms at the posterior edge of the basipterygium.
TO DO: reconcile cartilage elements of fin with bony elements (e.g. develops from and labeling).
Bilaterally paired small, rodlike cartilages on the ventral surface of the abdomen (present at 7.9 mm). Their posterior tips expand laterally, forming L-shaped cartilages. Medially, a posterior spur of cartilage develops, which will later ossify as the ischiac process (Weitzman 1962).
Small cartilage that forms at the posterior and medial edge of the basipterygium.
Small cartilage with a long posterior process and a shorter lateral one that forms at the posterior edge of the basipterygium, between radial cartilages 1 and 2.
Small cartilage that forms at the posterior and lateral edge of the basipterygium.
Pharyngeal arch cartilage that is the median cartilage of the ventral hyoid arch, generally lying between the paired ventral hypohyals.
Sublingual cartilage that is the ventral element paired with the sublingual dorsal cartilage.
Neural spine that is associated with the fourth vertebra.
Scute that is a bony plate that forms in the midline of ventral body margin between pectoral girdle and anal fin. Abdominal scutes may be present both anterior to and posterior to the pelvic girdle and fin.
Lepidotrichium which is part of the caudal fin.
Lepidotrichium which is part of the pectoral fin, forming the pectoral fin skeleton and articulating with the pectoral radials. A pectoral lepidotrichium is composed of two hemitrichia that surround bundles of actinotrichia distally.
Each pectoral lepidotrichium may be unsegmented (e.g., spine), segmented but unbranched (e.g., leading ray) or segmented and branched. Definition of lepidotrichium by Schultze and Arratia (1989: 217). For additional information about lepidotrichia see Arratia et al. 2001 and Arratia 2008.
Lepidotrichium which is part of the pelvic fin.
Dermal bone that is rod-like, formed and usually contained in a fin membrane, and jointed to or adjacent to distal radials. Lepidotrichia are formed from paired hemitrichia surrounding actinotrichia. There are usually two more lepidotrichia than distal radials.
Process of the premaxilla that extends posteriorly and overlays the mesethmoid.
In cypriniforms the anterior portion of the palatine has a dorsomedial process which abuts against the mesethmoid. Such a process is not present in other ostariophysans or in other primitive teleosts.
anterior dorsomedial process of autopalatine
Ural vertebra that is the second vertebra posterior to preural centrum 1. It may bear a rudimentary neural arch and sometimes a rudimentary spine or the neural arch and spine are completely absent and it may articulate or fuse with hypural 2 (polyural terminology). Ural vertebra 2 is an unpaired median bone.
Ural vertebrae 2 may be defined also as the second ural vertebrae bearing hypurals 3 or 3 and 4 or 3 plus more dorsal hypurals (diural terminology).
A vertebral centrum that is located immediately posterior to ural centrum 1. Ural centrum 2 is an unpaired median bone.
Ural centrum 2 (polyural terminology) may articulate or fuse with its neural arch dorsally or the neural arch may be absent, and with hypural 2 ventrally. Ural centrum 2 may be defined also as the second ural centrum bearing hypurals 3 or 3 and 4 or 3, 4 and more dorsal hypurals (diural terminology).
Urostyle that is the result of fusion of preural centrum 1 with the first ural centrum (of polyural terminology).
Caudal fin lepidotrichium that form part of the anterior dorsal and ventral series of lepidotrichia of the caudal fin that may be associated with a neural spine or an epural or an uroneural (dorsal series) and with a haemal spine of a preural vertebra (ventral series). Caudal procurrent rays are shorter than the caudal principal rays. A caudal procurrent ray is an unpaired median bone.
Caudal fin lepidotrichium that is adjacent to a branched ray. Caudal principal rays may be segmented but unbranched and the main element forming the dorsal or ventral leading margin of the caudal fin or a ray that may be only segmented-and-branched and forms part of the middle-posterior region of the fin. A caudal principal ray is an unpaired median bone.
Counts of caudal principal rays are taken as the number of branched rays plus two adjacent unbranched rays and counts are typically reported as, for example: 1,8,7,1 (1 unbranched and 8 branched upper rays, 7 branched and 1 unbranched lower rays). A caudal principal caudal ray may be associated with one or more hypurals or with hemal spines of preural centra 1 and 2 (Schultze and Arratia, 1989; Arratia, 2008). In basal teleosts the number of caudal principal rays is about 20. A decreasing of the number of the branched-and segmented rays is observed in more advanced teleosts (see Schultze and Arratia, 1989; Arratia, 1991, 2008).
pectoral fin radial element that is composed of bone tissue.
There are two paired series of pectoral radials, the proximal and the distal ones that may have variable shapes and sizes.
pectoral fin proximal radial element that is composed of bone tissue.
Two to four flat or slightly rod-like proximal pectoral radials, bilaterally, can be found in teleosts. Pectoral proximal radials are commonly hour-glass or rectangular shaped. The presence of four pectoral proximal radials is interpreted as a synapomorphy of teleosts (Patterson 1977, Arratia 1999).
pectoral fin distal radial element that is composed of bone tissue.
A variable number of pectoral distal radials may be present in each pectoral fin. They are commonly small elements, rod-like, round or square shaped.
The propterygium is the lateralmost or anteriormost basal cartilage that originates from the pectoral fin endoskeletal disc. The bases of the pectoral lepidotrichium 1 plus the propterygium articulates with the scapula.
The cartilaginous propterygium may partially ossify and fuse to the base of the pectoral hemilepidotrichium 1 in teleosts, but remains as a separate element in non-teleostean fishes.
Endochondral bone, membrane bone, and Weberian ossicle that is located dorsal to the scaphium. The claustrum bone is bilaterally paired.
Surface structure that is the dorsal portion of the caudal fin.
Surface structure that is the ventral portion of the caudal fin.
Process that is the upper portion of the maxilla that rests on the posterior surface of the lateral portion of the premaxilla.
Synonyms maxilla ascending arm used in Zanata and Vari 2005, and maxilla upper arm used in Weitzman 1962
Lateral bony projection proximal to lateral ethmoid-palatine joint, and located anterior to orbital region and posterior to olfactory region.
Scute that is a median bony plate forming anterior to procurrent caudal fin rays.
Process that is the paired process of the parasphenoid that articulates with the suspensorium.
Joint that articulates the autopalatine and lateral ethmoid and bones. Autopalatine-lateral ethmoid joint is paired.
Bony projection that is part of the pharyngobranchial 2 bone.
pharyngobranchial 2 bone uncinate process
An endochondral bone that is the dorsally-oriented bony extension of the quadrate, extending from the anterior portion of the bone.
Term from Weitzman, 1962 and Sidlauskas and Vari, 2008.
Process that is the posterior extension of the quadrate and located dorsal to the quadrate ventral process.
Multi-tissue structure that is a fluid-filled canal in the integument and usually dermal bones, and contains one or more neuromast organs.
Sensory canals usually communicate with the environment via pores in the sensory canal or at the distal ends of tubules, which extend from canal where pores would otherwise be.
dorsal fin middle radial element that is composed of bone tissue.
Synonym dorsal fin medial radial from Weitzman, 1962.
anal fin middle radial element that is composed of bone tissue.
Synonym anal fin medial radial from Weitzman, 1962.
Process of the sphenotic. The process may project antero-laterally or laterally or ventro-laterally and it has different development in different fish groups. The sphenotic spine is paired.
Superficial and lateral bony projection anterior to orbital region. Sometimes with superficial ornamentation where in direct contact with skin.
Synonym of lateral ethmoid wing: lateral ethmoid ventral wing (characiforms).
Sensory canal on trunk which is posterior to the pectoral girdle and often reaching to or onto the caudal fin. The trunk sensory canal is bilaterally paired.
Pores frequently piercing scales if present; occasionally enclosed in bony ossicles.
Sensory canal between and in close proximity to the trunk sensory canal and anteriorly with the otic and preoperculo-mandibular sensory canals. The post-otic sensory canal is bilaterally paired.
May be continuous with to the trunk sensory canal and anteriorly with the otic and preoperculo-mandibular sensory canals.
Anatomical cluster that consists of a bulla formed by the exoccipital and basioccipital bones, and surrounds the lagena.
Multi-tissue structure composed of enameloid and dentine surrounding a pulp cavity, and found either attached to dermal bone or freely in the skin.
Odontode that is attached to dermal bone.
Term from Schaefer & Buitrago-Suarez 2002.
Odontode that is attached to the skin and without association to dermal bone.
Tooth that is attached to the premaxilla.
Sensory canal between and in close proximity posteriorly with the post-otic and preoperculo-mandibular sensory canals, and anteriorly with the supraorbital and infraorbital sensory canals. The otic sensory canal is bilaterally paired.
May be continuous with the post-otic and preoperculo-mandibular sensory canals, and anteriorly with the supraorbital and infraorbital sensory canals.
Sensory canal that crosses over the dorsal midline and in close proximity to the contralateral post-otic sensory canals. The supratemporal sensory canal is unpaired.
Tooth that is attached to the ectopterygoid bone.
Tooth that is attached to the entopterygoid bone.
Most anterior pharyngobranchial cartilage, located medial to the epibranchials.
Most anterior pharyngobranchial bone, located medial to the epibranchials.
Most posterior pharyngobranchial bone, located medial to the epibranchials.
Perichordal bone that surrounds the anterior tip of the notochord.
Dermal bone of the pharyngeal arches usually bearing teeth.
Pharyngeal tooth plate that lies dorsal to the basihyal cartilage or bone.
Tooth that is attached to the basihyal tooth plate.
Pharyngeal tooth plate that lies ventral to pharyngobranchial 2 bone.
Tooth that is attached to the pharyngobranchial 2 tooth plate.
Pharyngeal tooth plate that lies ventral to pharyngobranchial 3 bone.
Tooth that is part of the pharyngobranchial 3 tooth plate.
Pharyngeal tooth plate that lies ventral to pharyngobranchial 4, and located anterior to upper pharyngeal 5 tooth plate.
Tooth that is attached to the upper pharyngeal 4 tooth plate.
Pharyngeal toothplate that lies ventral to pharyngobranchial 4, and located posterior to upper pharyngeal 4 tooth plate.
Tooth that is attached to the upper pharyngeal 5 tooth plate.
Pharyngeal tooth plate that lies ventral to pharyngobranchials 3 and 4.
This represents the condition found in catfishes.
Tooth that is attached to the upper pharyngeal tooth plate.
Tooth that is part of the basibranchial tooth plate.
Pharyngeal tooth plate that lies dorsal to basibranchials 1-3.
Pharyngeal tooth plate that lies dorsal to basibranchial 4 bone.
Tooth that is attached to the basibranchial 4 tooth plate.
Pharyngeal tooth plate that lies dorsal to basibranchial 2 bone.
Tooth that is attached to the basibranchial 2 tooth plate.
Neural arch on the urostyle. It does not support a neural spine. Sanger and McCune 2002.
anal fin radial element that is composed of bone tissue.
dorsal fin radial element that is composed of bone tissue.
Infraorbital that is the sixth bone of the infraorbital series.
Bony projection that extends from the mesethmoid anteriorly. Mesethmoid cornua are paired processes each articulating with its ipsilateral premaxilla and both cornua bounding a median mesethmoid cleft.
Joint that articulates the mesethmoid and premaxilla. Mesethmoid-premaxillary joint is paired.
Joint that articulates the mesethmoid and nasal. Mesethmoid-nasal joint is paired.
Joint that articulates the mesethmoid and frontal. Mesethmoid-frontal joint is paired.
Joint that articulates the mesethmoid and lateral ethmoid. Mesethmoid-lateral ethmoid joint is paired.
Joint that articulates the mesethmoid and vomer. Mesethmoid-vomer joint is unpaired.
Bony projection that is mesially-directed and off the anteromedial corner of each mesethmoid cornu.
Ligament that is attached to supracleithrum and basioccipital.
Membrane bone that is fused to supracleithrum and is jointed to basioccipital and exoccipital.
Lateral ethmoid-ectopterygoid ligament is a ligament that connects the lateral ethmoid to the ectopterygoid.
The bony shelf above orbit is an anatomical cluster formed by the dorsolateral portions of the lateral ethmoid, frontal and sphenotic bones that forms the dorsal margin of the orbit.
Interopercular-mandibular ligament is a ligament that connects the interopercle to an element of the lower jaw, typically the retroarticular.
palatine cartilage - cartilage that is separate from and anterior to the pterygoquadrate cartilage.
pterygoquadrate cartilage - cartilage that is separate from and posterior to the palatine cartilage.
anterior cartilage of palatine - cartilage that caps the anterior end of the autopalatine bone. It is typically present in adults.
posterior cartilage of palatine - cartilage that caps the posterior end of the autopalatine bone. It is typically present in adults.
Dermal bone that is located in the middle of the upper jaw, independently formed by fusion of tooth bases attached to soft tissue in the middle portion of the upper lip. The median premaxilla bears teeth in adults.
Recorded in trichomycterid subfamilies Stegophilinae and Vandelliinae (Baskin, 1973). submitted by Mario de Pinna.
Muscle located in the lateral region of the cheek, linking the lateral surface of opercle with the posterolateral margin of the suspensorium (usually the preopercle).
Occurs in most members of the Trichomycteridae, except in basal Copionodontinae and Trichogeninae (de Pinna, 1992).
Ligament that links the tip of the postcleithral process of the cleithrum with either the vertebral column (at the vertebral parapophysis or rib of the sixth vertebra) or with the soft tissue around the postcleithral region.
Recorded in siluriform families Aspredinidae, Amblycipitidae, Akysidae, Sisoridae and Erethistidae (dePinna 1996). Submitted by Mario de Pinna.
Pharyngeal arch cartilage, elongate and usually bifurcated posteriorly, located anteriorly on the upper branchial arches, attached to the anterior tips of the first infrapharyngobranchials. It supports rows of gill rakers on each side and is not homologous to other structures in the teleost gill-arch skeleton. One or two mediopharyngobranchials may be present.
Recorded in several Clupeoidei (Nelson, 1967). Submitted by Mario de Pinna.
Pharyngeal arch cartilage present on the dorsal surface of the middle portion of the upper branchial arches, dorsal to the point of contact between the second and third infrapharyngobranchials. It is round or cylyndrical in shape. Not homologous to the mediopharyngobranchial.
Recorded in Pristigasteridae and Engraulidae, of Clupeiformes, apparently also present in Chanos, of Gonorynchiformes (Di Dario, 2002).
Endochondral bone, which may be ossified or not in adults, located immediately anteriorly to the pterygiophore series of the anal fin. The structure is usually cylindrical, and its plane of symmetry is transverse to that of pterygiophores and fin rays.
Recorded in some Cetopsidae, Clariidae and Austroglanididae (Siluriformes) (De Pinna et al., 2007).
Endochondral bone located posterior to the last anal fin pterygiophore. The anal fin stay is a median bone.
Endochondral bone located posterior to the last dorsal fin pterygiophore. The dorsal fin stay is a median bone.
Dermal bone that is located anterior to the caudal fin procurrent rays. Caudal fin stays are unpaired median bones.
Development of caudal fin stays appears uncertain according to several authors (e.g., Zanata and Vari 2005, Vari 1995).
Basibranchial bone that is ventral, median, and associated with branchial arch 5 (pharyngeal arch 7). Develops in posterior copula cartilage or basibranchial 5 cartilage.
Infraorbital that is the seventh bone of the infraorbital series.
Infraorbital that is the eighth bone of the infraorbital series.
Infraorbital that is the ninth bone of the infraorbital series.
Infraorbital that is the tenth bone of the infraorbital series.
Infraorbital that is the eleventh bone of the infraorbital series.
Infraorbital that is the twelfth bone of the infraorbital series.
Infraorbital that is the last bone of the infraorbital series, carrying the infraorbital canal, and sometimes also the supraorbital, temporal, and/or preopercular canals. The dermosphenotic is sometimes sutured or fused completely to the skull, e.g. to the autosphenotic.
Anatomical cluster that is the series of dermal bones surrounding the orbit and associated with the infraorbital sensory canal.
The infraorbital series may include the antorbital, a variable number of infraorbitals, and dermosphenotic (or posteriormost dorsal infraorbital). The infraorbital series may be formed by seven (primitively) or less bones in teleosts. Consequently, the so called dermosphenotic may correspond to the seventh, sixth or fifth bone, etc., depending on the taxon.
Joint that articulates the opercle and interopercle. Opercle-interopercle joint is paired.
Joint that articulates the frontal and pterotic. Frontal-pterotic joint is paired.
Caudal principal ray that is the dorsalmost caudal principal ray of the caudal fin.
For reference, see Weitzman and Fink 1985 Figure 8.
Caudal principal ray that is ventrally adjacent to caudal principal ray 1.
Caudal principal ray that is ventrally adjacent to caudal principal ray 2.
Caudal principal ray that is ventrally adjacent to caudal principal ray 3.
Caudal principal ray that is ventrally adjacent to caudal principal ray 4.
Caudal principal ray that is ventrally adjacent to caudal principal ray 5.
Caudal principal ray that is ventrally adjacent to caudal principal ray 6.
Caudal principal ray that is ventrally adjacent to caudal principal ray 7.
Caudal principal ray that is ventrally adjacent to caudal principal ray 8.
Caudal principal ray that is ventrally adjacent to caudal principal ray 9.
Caudal principal ray that is ventrally adjacent to caudal principal ray 10.
Caudal principal ray that is ventrally adjacent to caudal principal ray 11.
Caudal principal ray that is ventrally adjacent to caudal principal ray 12.
Caudal principal ray that is ventrally adjacent to caudal principal ray 13.
Caudal principal ray that is ventrally adjacent to caudal principal ray 14.
Caudal principal ray that is ventrally adjacent to caudal principal ray 15.
Caudal principal ray that is ventrally adjacent to caudal principal ray 16.
Caudal principal ray that is ventrally adjacent to caudal principal ray 17.
Caudal principal ray that is ventrally adjacent to caudal principal ray 18.
Vertebra that is posteriorly adjacent to vertebra 4.
Bony projection that is the posterolaterally oriented projection on the ventral region of the mesethmoid. Mesethmoid ventral diverging lamellae are paired and posteriorly contact the lateral ethmoid bones.
Process that is the posteriorly oriented, paired projection of the basipterygium.
Foramen that is located in the scapula. The scapular foramen is paired and formed by a ring of bone.
Foramen that is located in the coracoid.
Fontanel that is located between the contralateral frontals and anterior to the epiphyseal bar.
Fontanel that is located posterior to the epiphyseal bar, and typically located between the contralateral frontals and parietals (if present) and bordered posteriorly by the supraoccipital.
Foramen through which branches of cranial nerves V (trigeminal) and VII (facial) exit.
i]In some vertebrates there are separate trigeminal foramen and facial foramen.
Foramen through which cranial nerve VIII (auditory) exits.
Anatomical space within a bone in which teeth develop.
Replacement tooth trench that is located in the premaxilla.
Replacement tooth trench that is located in the dentary.
Bony projection located on the anteroventral region of the mesethmoid which articulates with the premaxilla.
Synonyms: mesethmoid lateral wing (Zanata and Vari 2005) lateral ethmoid wing (Weitzman 1962) premaxillary articular process (Fink and Fink 1996).
Foramen through which the superficial ophthalmic nerve passes.
Joint that articulates the dentary and anguloarticular. Dentary-anguloarticular joint is paired.
Rib that articulates with the parapophysis of the sixth centrum.
Rib that articulates with the parapophysis of the fifth centrum.
The pre-narial cartilage is a cartilage that is located anterior to the anterior naris.
Fossa where the exoccipital forms the medial portion and the epioccipital forms the lateral margin.
Chen 1994 gives these two synonyms: 'temporal fossa', Gauba 1967; and 'temporal groove', Mahajan 1966.
Pectoral fin lepidotrichium 1 is the leading or marginal ray of the fin and articulates with the scapula. Lepidotrichium 1 is commonly segmented but unbranched but occasionally may be a massive strong unsegmented element (e.g., spine).
Pectoral fin lepidotrichium that, in a linear sequence, is the second most anterior pectoral ray that it is usually branched and segmented.
Pectoral fin lepidotrichium that, in a linear sequence, is the third most anterior pectoral ray that it is usually branched and segmented.
Pectoral fin lepidotrichium that, in a linear sequence, is the fourth most anterior pectoral ray that it is usually branched and segmented.
Pectoral fin lepidotrichium that, in a linear sequence, is the fifth most anterior pectoral ray that it is usually branched and segmented.
Pectoral fin lepidotrichium that, in a linear sequence, is the sixth most anterior pectoral ray that it is usually branched and segmented.
Pectoral fin lepidotrichium that, in a linear sequence, is the seventh most anterior pectoral ray that it is usually branched and segmented.
Bilaterally paired dorsal hyoid arch muscle that retracts the maxillary barbel.
Process that is part of the supraoccipital. It is a posteriorly directed and unpaired median projection off the posterior margin of the supraoccipital bone.
The supraoccipital crest may be small and restricted to the dorsal part of the supraoccipital, or may be large and long and extending ventrally to the dorsal margin of the foramen magnum. The supraoccipital crest may be a large process extending above the skull roof in some teleostean subgroups.
Joint that articulates autopalatine and vomer bones. Autopalatine-vomer joint is paired.
Pectoral-fin lepidotrichium 1 with mostly co-ossified and unsegmented hemitrichia that form a stiff and usually thick shaft and enlarged basal processes that moveably articulate with the pectoral girdle. The pectoral fin spine may also result from the fusion of several lepidotrichia that form a stiff shaft.
Dermal bone that is located near the lateral margin of the pelvic fin, and lateral to pelvic-fin lepidotrichium 1.
Dorsal-fin lepidotrichium 1 with co-ossified and unsegmented hemitrichia that form a stiff shaft and enlarged base that moveably articulates with first (anteriormost) dorsal-fin pterygiophore.
Dorsal-fin lepidotrichium 2 with co-ossified and unsegmented hemitrichia that form a stiff shaft and enlarged base that moveably articulates with second dorsal-fin pterygiophore.
Bony projection that is part of the pharyngobranchial 3.
pharyngobranchial 3 bone uncinate process
Bony projection that is part of the pharyngobranchial 4.
infrapharyngobranchial 4 bone uncinate process
pharyngobranchial 4 bone uncinate process
Joint that articulates orbitosphenoid and prootic bones. Orbitosphenoid-prootic joint is paired.
Foramen in the anterior ceratohyal for passage of the hyoidean artery.
Epibranchial uncinate process that is part of epibranchial 2 bone.
Epibranchial uncinate process that is part of epibranchial 1 bone.
Intermuscular bone that articulates with the vertebral centrum.
Intracranial space formed by confluence of supraorbital, infraorbital, preopercular and temporal sensory canals. See also Di Dario (2004).
Modified epicentral intermuscular bone that connects the back of the skull with the pectoral girdle.
Joint that articulates quadrate and hyomandibula bones. Quadrate-hyomandibula joint is paired.
Joint that articulates quadrate and metapterygoid bones. Quadrate-metapterygoid joint is paired.
Foramen for the passage of the olfactory nerve or cranial nerve 1.
Endochondral bone that is located posterior to the dentary, medial to the angular and antero-dorsal to the retroarticular forming the lower jaw. The articular bears a dorso-posterior articular facet for the condyle of the quadrate. The articular is a paired bone.
The articular fuses with the angular bone in clupeocephalans forming the anguloarticular.
An anterior extension of the swimbladder that passes through a foramen in the exoccipital; part of the otophysic connection between swimbladder and inner ear.
intracranial diverticulum of swimbladder
Fossa that is a concavity on the dorsolateral surface of the skull roof found at least partially on the epiotic (epioccipital).
Foramen through which cranial nerve VII (facial) exits.
anterior opening trigeminofacialis chamber
This is the anterior opening of the trigeminofacialis (or trigeminal-facialis) chamber.
Foramen through which cranial nerve V (trigeminal) exits.
posterior opening of trigeminofacialis chamber
This is the posterior opening of trigeminofacialis (or trigeminal-facialis) chamber.
Sensory canal anterior to and in close proximity to the otic and infraorbital sensory canals. The supraorbital sensory canal is bilaterally paired.
May be continuous with otic and infraorbital sensory canals.
Sensory canal lateral or ventral to and in close proximity to the otic and supraorbital sensory canals at their union. The infraorbital sensory canal is bilaterally paired and associated with the infraorbital bones.
May be continuous with otic and supraorbital sensory canals at their union.
Sensory canal lateral or ventral to and in close proximity to the otic and post-otic sensory canals at their union. The preoperculo-mandibular sensory canal is bilaterally paired and associated with the preopercle, angular and dentary bones.
May be continuous with the otic and post-otic sensory canals at their union.
Sensory canal lateral or ventral to and in close proximity with the otic and post-otic sensory canals at their union, and anteroventrally with the mandibular sensory canal. The preopercular sensory canal is bilaterally paired and associated with the preopercle bone.
Sensory canal anterior and ventral to and in close proximity with the preoperculo-mandibular sensory canal. The mandible sensory canal is bilaterally paired and associated with the angular and dentary bones.
May be continuous with the preoperculo-mandibular sensory canal.
Dermal bone that is a bony expansion in the integument anterior to or flanking the dorsal fin that is part of and at the distal end of a supraneural or dorsal fin proximal radial.
Nuchal plate that is unpaired and part of the supraneural and in contact, or not, with the supraoccipital crest anteriorly and middle nuchal plate posteriorly.
Nuchal plate that is unpaired and part of dorsal fin proximal radial 1 and usually in contact with the anterior nuchal plate and paired posterior nuchal plates.
dorsal fin proximal radial 1 element that is composed of bone tissue.
dorsal fin proximal radial 2 element that is composed of bone tissue.
Paired nuchal plate that is part of dorsal fin proximal radial 2 and usually in contact with the middle nuchal plate.
Portion of tissue that is part of the caudal fin.
Epibranchial uncinate process that is part of epibranchial 3 bone.
Epibranchial uncinate process that is part of epibranchial 4 bone.
Scale that is associated with the lateral line sensory canal.
Process that is part of the urohyal; it is the posterolaterally directed process located on the ventrolateral margin of urohyal. Urohyal lateral process is paired.
Synonyms: urohyal lateral lamella (Toledo-Piza 2007; Zanata and Vari 2005) urohyal ventral wing (Castro and Vari 2004).
Process that is part of the urohyal; it is the posterodorsally directed and median process located on the dorsal margin of the urohyal.
Ligament that connects the premaxilla to the maxilla.
Ligament that connects the maxilla with the lower jaw.
Synonym articular-maxillary ligament (Alexander 1964).
Caudal procurrent ray that forms part of the anterior dorsal series of lepidotrichia of the caudal fin and may be associated with a neural spine or a epural or a uroneural. A pair of hemitrichia forms each ray.
Caudal procurrent ray that forms part of the anterior ventral series of lepidotrichia of the caudal fin that may be associated with a neural spine or a epural or an uroneural (dorsal series) and with a hemal spine of a preural vertebra (ventral series). A caudal procurrent ray is an unpaired median bone.
Joint that articulates the pterosphenoid and orbitosphenoid. Pterosphenoid-orbitosphenoid joint is paired.
Joint that articulates the parasphenoid and basioccipital. Parasphenoid-basioccipital joint is unpaired.
Anatomical point that is the apex of a projection or anything long and tapered; can be bony or cartilage
Joint that articulates the interhyal and epihyal bones, or interhyal and ceratohyal cartilages. Interhyal-epihyal joint is paired.
Logical definition to be added after generic element classes added to group/bone cartilage
Joint that articulates the epihyal and ceratohyal bones. Epihyal-ceratohyal joint is paired.
Joint that articulates the ceratohyal and dorsal hypohyal bones. Ceratohyal-dorsal hypohyal joint is paired.
Joint that articulates the ceratohyal and ventral hypohyal bones. Ceratohyal-ventral hypohyal joint is paired.
Joint that articulates the dorsal hypohyal and ventral hypohyal bones. Dorsal hypohyal-ventral hypohyal joint is paired.
Joint that articulates the contralateral ventral hypohyal bones or the contralateral ceratobranchial cartilages. Inter-ventral hypohyal joint is paired.
Joint that articulates the dorsal hypohyal and urohyal bones. Dorsal hypohyal-urohyal joint is paired.
Joint that articulates the ventral hypohyal and urohyal bones. Ventral hypohyal-urohyal joint is paired.
Joint that articulates the epihyal and branchiostegal ray bones. Epihyal-branchiostegal ray joint is paired.
Joint that articulates the ceratohyal and branchiostegal ray bones. Ceratohyal-branchiostegal ray joint is paired.
Postcleithrum that anteriorly articulates with the supracleithrum and/or the cleithrum of the pectoral girdle; most dorsal element in a series of postcleithra.
Postcleithrum that articulates dorsally with postcleithrum 1, ventrally with postcleithrum 3, and anteriorly with cleithrum.
Postcleithrum that articulates dorsally with postcleithrum 2 and, sometimes, anteriorly with cleithrum.
Process on the dorso-posterior margin of the hyomandibula cartilage or bone that articulates with a depression on the antero-dorsal margin of the opercle.
Gill ray is a slender, usually rod-like cartilage within a gill filament and ligamentously tied to its associated pharyngeal arch bone or cartilage.
An artery that passes along the ventral portions of the hyoid arch; supplies oxygenated blood to the pseudobranch.
A pharyngobranchial bone that articulates with the neurocranium dorsally and epibranchial 1 and pharyngobranchial 2 ventrally; lies dorsal to other elements of the dorsal portions of the branchial arches.
Articulates with the exoccipital or prootic depending on taxon.
Pharyngeal tooth plate that lies ventral to pharyngobranchial 1 bone.
Joint that articulates the epibranchial 4 cartilage or bone and upper pharyngeal toothplate. Epibranchial 4-upper pharyngeal toothplate joint is paired.
epibranchial 4-upper pharyngeal toothplate joint
Joint that articulates the epibranchial 3 cartilage or bone and pharyngobranchial 3 cartilage or bone. Epibranchial 3-pharyngobranchial 3 joint is paired.
epibranchial 3-pharyngobranchial 3 joint
Joint that articulates the epibranchial 3 cartilage or bone and pharyngobranchial 4 cartilage or bone. Epibranchial 3-pharyngobranchial 4 joint is paired.
epibranchial 3-pharyngobranchial 4 joint
Joint that articulates the left and right hypobranchial 3 cartilages or bones. Inter-hypobranchial 3 joint is unpaired.
Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 1 (pharyngeal arch 3).
Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 4 (pharyngeal arch 6).
Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 5 (pharyngeal arch 7).
Pharyngeal arch cartilage that is ventral, median, and at or posterior to the juncture of the bilaterally paired ceratobranchial 5 cartilage or bone.
Postcranial axial cartilage located dorsal to vertebra 2.
Postcranial axial cartilage located dorsal to vertebrae 3 and 4.
Anatomical cluster that consists of the Weberian ossicles.
Lateral line system on head and pectoral girdle.
Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 2 (pharyngeal arch 4).
Pharyngeal arch cartilage that is ventral, median, and associated with branchial arch 3 (pharyngeal arch 5).
Neural arch that is the anteriormost neural arch.
Rib that articulates with the parapophysis of the second centrum.
Rib that articulates with the parapophysis of the first centrum.
Rib that articulates with the parapophysis of the third centrum.
Rib that articulates with the parapophysis of the fourth centrum.
parapophysis + rib of vertebra 3 + rib of vertebra 4
Neural arch that is located posterior to the neurocranium and anterior to neural arch 1. The accessory neural arch is not associated with a vertebral centrum.
Definition from de Pinna and Grande (2003).
Neural spine that is associated with the first vertebra.
Neural spine that is associated with the second vertebra.
Neural spine that is associated with the third vertebra.
Supraneural bone located dorsal to vertebra 1.
Postcranial axial cartilage located dorsal to vertebra 1.
Skeletal element that is bilaterally paired and articulates dorsally with the hyosymplectic cartilage or the articulation of the hyomandibula and symplectic.
Skeletal element that is bilaterally paired and articulates medially with a median skeletal element and laterally with a ceratobranchial element.
Skeletal element that is ventral, bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 1 element laterally.
Skeletal element that is ventral, bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 2 element laterally.
Skeletal element that is ventral, bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 3 element laterally.
Skeletal element that is ventral, bilaterally paired and articulates with a median skeletal element medially and with a ceratobranchial 4 element laterally.
Skeletal element that is bilaterally paired and forms part of the ventral branchial arches.
Skeletal element that is bilaterally paired and articulates laterally with ceratobranchial element.
Skeletal element of the branchial arches located medial to the epibranchials.
Most anterior pharyngobranchial element, located medial to the epibranchials.
Pharyngobranchial element, located medial to the epibranchials and posteriorly adjacent to pharyngobranchial 1 element.
Pharyngobranchial element, located medial to the epibranchials and posteriorly adjacent to pharyngobranchial 2 element.
Most posterior pharyngobranchial element, located medial to the epibranchials.
Skeletal element that is median and associated with branchial arch 1.
Skeletal element that is median and associated with branchial arch 2.
Skeletal element that is median and associated with branchial arch 3.
Skeletal element that is median and associated with branchial arch 4.
Skeletal element that is median and associated with branchial arch 5.
Anatomical structure that is formed as a hiatus in the muscles covering the anterior chamber of the swim bladder in the area of ribs 5 and 6.
Surface structure that is a fleshy membrane covering part of the eye.
Joint between the left and right frontal bone.
Foramina that allow passage of occipital arteries.
Foramen for passage of nerve supplying otic lateral line.
Fossa or chamber on posterior portion of orbital region of neurocranium that serves as attachment site for posterior extrinsic eye muscles.
Fossa or chamber on anterior portion of orbital region of neurocranium that serves as attachment site for anterior extrinsic eye musculature.
Fossa of opercle that articulates with hyomandibular condyle for opercle.
Process of the epioccipital that extends posteriorly, is laminar in form and is usually attached to Weberian apparatus.
Dermal bone that is located lateral to vomer off midline of palate. Accessory vomerine tooth plate bears teeth and may be present as one or more pairs.
Accessory vomerine tooth plate is not synonymous with dermopalatine tooth plate, palatine tooth plate, or pterygoid tooth plate.
Scute that is an elongated plate associated with a ligament running between posterior nuchal plate and rib on vertebra 6. Infranuchal scute is paired and develops from its associated ligament and sensory canal tubular ossicle.
Dermal bone that is ring-shaped or cylindrical and surrounds a sensory canal.
Sensory canal that is a side branch between a sensory canal proximally and a pore at its distal end. Sensory canal tubule is bilaterally paired although often imperfectly so.
Dermal bone that is located on midline of snout in skin above mesethmoid and lateral ethmoid bones. Rostral plate bears type 1 odontodes and is unpaired.
Lip that is expanded to form a broad, rounded cup around the mouth.
Barbel that is attached to the anterior rim of the posterior nostril. Posterior nasal barbel is paired.
Barbel that is associated with the anterior nostril. Anterior nasal barbel is paired.
Barbel that is attached to the distal end of the maxilla and that originates on the side of the mouth. Maxillary barbel is paired.
Joint that articulates the left and right basipterygium cartilage or bone. Inter-basipterygium joint is unpaired.
Joint between the centra, and sometimes the neural arches or parapophyses of vertebra 4 and vertebra 5.
Joint that articulates the orbitosphenoid cartilage or bone and lateral ethmoid cartilage or bone. Orbitosphenoid-lateral ethmoid joint is paired.
Joint that articulates the autopalatine cartilage or bone and maxilla.
Ligament that connects the metapterygoid to the autopalatine.
Lateral ethmoid-autopalatine ligament is a ligament that connects the lateral ethmoid to the autopalatine.
Mesethmoid-premaxillary ligament is a ligament that connects the mesethmoid to the premaxilla.
Mesethmoid-maxillary ligament is a ligament that connects the mesethmoid to the maxilla.
Joint that articulates the hyomandibular cartilage or bone and otic region cartilage or sphenotic bone, and often pterotic bone and prootic bone. Hyomandibular-otic region joint is paired.
Process that is part of the anal fin lepidotrichium.
Process that is part of the caudal fin lepidotrichium.
Caudal fin hook is found in some characiform fishes.
Joint that articulates the left and right premaxillary bones. Inter-premaxillary joint is unpaired.
Surface structure that is a portion of skin that projects or hangs from the body.
Pharyngeal cartilage that is part of and at the proximal end of epibranchial 1 bone, and that usually articulates with a pharyngobranchial element. Epibranchial 1 bone proximal cartilage is paired.
Pharyngeal cartilage that is part of and at the proximal end of epibranchial 2 bone, and that usually articulates with a pharyngobranchial element. Epibranchial 2 bone proximal cartilage is paired.
Pharynbeal cartilage that is part of and at the distal end of ceratobranchial 3 bone, and that usually articulates with epibranchial 3 element. Ceratobranchial 3 bone distal cartilage is paired.
ceratobranchial 3 bone lateral cartilage
ceratobranchial 3 bone posterior cartilage
Pharyngeal cartilage that is part of and at the proximal end of ceratobranchial 4 bone, and that usually articulates with basibranchial 4 element. Ceratobranchial 4 proximal cartilage is paired.
ceratobranchial 4 bone anterior cartilage
ceratobranchial 4 bone proximal cartilage
Pharyngeal cartilage that is part of and at the distal end of ceratobranchial 4 bone, and that usually articulates with epibranchial 4 element. Ceratobranchial 4 distal cartilage is paired.
ceratobranchial 4 bone lateral cartilage
ceratobranchial 4 bone posterior cartilage
Pharyngeal cartilage that is part of and at the distal end of ceratobranchial 5 bone. Ceratobranchial 5 bone distal cartilage is paired.
ceratobranchial 5 bone lateral cartilage
ceratobranchial 5 bone posterior cartilage
Pharyngeal cartilage that is part of and at the distal end of hypobranchial 1 bone, and that usually articulates with ceratobranchial 1 element. Hypobranchial 1 bone distal cartilage is paired.
hypobranchial 1 bone posterior cartilage
Pharyngeal cartilage that is part of and at the distal end of hypobranchial 2 bone, and that usually articulates with ceratobranchial 2 element. Hypobranchial 2 bone distal cartilage is paired.
hypobranchial 2 bone posterior cartilage
Pharyngeal cartilage that is part of and at the distal end of epibranchial bone 3 uncinate process. epibranchial bone 3 uncinate process cartilage is paired.
epibranchial 3 bone uncinate process cartilage
Pharyngeal cartilage that is part of and at the distal end of epibranchial bone 4 uncinate process. Epibranchial bone 4 uncinate process cartilage is paired.
epibranchial 4 bone uncinate process cartilage
Obsoleted as we redundant with other classes. See https://github.com/obophenotype/uberon/issues/462
Mental barbel that originates on the chin, in a posterolateral position relative to the inner mental barbel.
Mental barbel that originates on the chin, in an anteromedial position relative to the outer mental barbel. The inner mental barbel is nearer to the mandibular symphysis than is the outer mental barbel.
Parapophysis that is the lateral projection from the fourth centrum. Parapophysis 4 is bilaterally paired.
Ligament that connects one rib to another.
Anatomical cluster composed of one or more bones and tissue that separates the orbits.
Surface structure that is a portion of the integument thickened relative to surrounding area.
Joint that articulates the hyomandibula bone and metapterygoid bone.
Vertebra that is posteriorly adjacent to vertebra 6.
Vertebra that is posteriorly adjacent to vertebra 7.
Pharyngeal arch cartilage that is a spherical mass of cartilage located between the mandibular symphysis and ventral hyoid arch. Mandibular-hyoid median cartilage is unpaired.
hyomandibular cartilage sensu Schaefer (1990)
Schaefer, S. 1990. (Anatomy and relationships of the scoloplacid catfishes. Proc. Acad. Nat. Sci. Phil. 142: 167-210) described this structure in certain catfishes and applied the name hyomandibular cartilage. To avoid possible confusion of this structure with the hyomandibular cartilage (or bone) of the suspensorium, the term mandibular-hyoid median cartilage is used here.
Anatomical cluster that is an outgrowth of the soft tissue around the dorsolateral corner of a branchial arch that is internally supported by a core of rigid cartilage-like tissue. Epibranchial arborescent organ is paired.
Greenwood, P. H. 1961 (A revision of the genus Dinotopterus Blgr. (pisces, Clariidae) with notes on the comparative anatomy of the suprabranchial organs in the Clariidae. Bull. British Mus (Nat. His.), Zool. 7(4): 217-241.) described this structure in certain catfishes and applied the term suprabranchial organ to it. To avoid possible confusion with distinctly different structures bearing the name suprabranchial organs in other teleosts, the term epibranchial arborescent organ is used here following the lead of de Pinna 1993.
Membrane bone extending between a transverse process of the second proximal dorsal-fin radial and the pleural rib of the sixth vertebra. Lateral bone is paired.
Anal fin lepidotrichium that is distally branched.
Pectoral fin lepidotrichium that is distally branched and segmented.
Anatomical cluster that consists of adjacent gill rakers constituting a row and is part of a ceratobranchial or epibranchial element of the branchial arches. Gill raker row is paired.
Surface structure that is a small, fleshy protuberance.
Compound dermal and endochondral bone that results from the fusion of the paired dermal parietal bones and the median endodermal supraoccipital. Forms the dorso-posterior element of the dermatocranium.
A parietal-supraoccipital or parieto-supraoccipital bone is an element present in Siluriformes.
Dermal bone that results from the fusion of the dermal posttemporal and the dermal supracleithrum. Forms the upper skeletal element of the pectoral girdle between the cleithrum and neurocranium. Posttemporal-supracleithrum is paired.
A posttemporo-supracleithrum is a bone present in Siluriformes. There are different opinions if this is the result of an ontogenetic or a phylogenetic fusion or the loss or one or other bone.
Process arising from the posterior or postero-dorsal margin of the cleithrum dorsally adjacent to the insertion of the pectoral fin. Posterior cleithral process is paired.
Process that is tooth-like or thorn-like and arising from the posteriorly-facing margin of the abducted pectoral spine.
posterior denticle of pectoral fin spine
posterior serration of pectoral fin spine
posterior dentation of pectoral fin spine
Process that is tooth- or thorn-like and arising from the anteriorly-facing margin of the abducted pectoral spine. Anterior dentation of pectoral fin spine is usually present on the proximal and/or middle section of the pectoral fin spine.
anterior serration of pectoral fin spine
anterior dentation of pectoral fin spine
Process that is retrorse, thorn-like and arising from the anteriorly-facing margin of the abducted pectoral spine. Anterior distal serration of pectoral fin spine is usually present on the distal section of the pectoral fin spine.
pectoral fin spine anterior distal serration
anterior distal serration of pectoral fin spine
Process that is tooth or thorn-like and arising from the posteriorly-facing margin of the abducted dorsal-fin spine 2.
posterior denticle of dorsal fin spine 2
posterior serration of dorsal fin spine 2
posterior dentation of dorsal fin spine 2
Process that is tooth- or thorn-like and arising from the anteriorly-facing margin of the abducted dorsal-fin spine 2.
anterior serration of dorsal fin spine 2
anterior dentation of dorsal fin spine 2
Dermal bone that is ventral to the preopercle and bears a portion of the preopercular sensory canal.
The number of canal plates present can be variable.
Pore that is located ventral to the posterior cleithral process and medial to the pectoral fin. Axillary pore is at the end of a duct from an integumentary gland.
Neural lamina is a median, vertical ridge or bony septum between neural spine 3 and neural spine 4 on the dorsal side of the Weberian vertebra. Neural lamina is unpaired.
Pharyngeal cartilage that caps the medial margin of the palatine at the autopalatine-lateral ethmoid joint.
Nerve that is a branch of cranial nerve VII that passes through or around the suspensorium to innervate muscles and sensory organs on or near pharyngeal arch 2.
Fontanel within the frontal bone near the frontal-sphenotic joint. Lateral fontanel of frontal is paired.
Original reference: de Pinna MCC, Vari RP. 1995. Monophyly and phylogenetic diagnosis of the family Cetopsidae, with synonymization of the Helogenidae (Teleostei: Siluriformes). Smithsonian Contributions to Zoology 571: 1-26.
Foramen located on the dentary for passage of the mandibular nerve.
Process that is the dorsally directed portion of ceratobranchial 5 bone.
An ascending limb of the ceratobranchial is found in Cypriniformes.
ascending limb of ceratobranchial 5 bone
Process that is the dorsally directed portion of ceratobranchial 5 cartilage.
ascending limb of ceratobranchial 5 cartilage
Dermal bone of upper pharyngeal arches associated with pharyngobranchial bones or cartilages, usually bearing teeth.
Pharyngeal tooth plate that lies ventral to pharyngobranchial 4.
Process that is the anterior and medially directed portion of ceratobranchial 5 bone part of ceratobranchial 5 bone.
This term applies to cypriniform fishes.
Process that is the anterior and medially directed portion of ceratobranchial 5 cartilage.
anterior limb of ceratobranchial 5 cartilage
Bone that is a fusion of the pterotic, posttemporal, and supracleithrum bones.
Dermal bone bearing teeth located between the distal end of the premaxilla and the middle of the maxilla. The hypomaxilla is a paired bone.
Hypomaxilla is a bone restricted to some clupeiforms. See Berry (1964) for a detailed account of the distribution of the hypomaxilla within clupeiforms and specifically in Herengula.
Process that is the lateral projection of the parasphenoid arising and articulating with the more dorsal portions of the neurocranium, usually at the level of the prootic.
Dermal bone of the dorsal surface of the olfactory region. Dermethmoid can be paired or median.
Endochondral bone found between the preethmoid and maxilla.
pectoral fin proximal radial 1 element that is composed of bone tissue.
pectoral fin proximal radial 2 element that is composed of bone tissue.
pectoral fin proximal radial 3 element that is composed of bone tissue.
pectoral fin proximal radial 4 element that is composed of bone tissue.
Process on the ventral surface of the horizontal limb of the coracoid, close to and parallel to the coracoid-cleithrum joint. Ventral keel of coracoid is paired.
Foramen in the bone or cartilage comprising the anterior wall of the orbit, and through which passes at least the deep ophthalmic branch of cranial nerve V (trigeminal).
Joint that articulates the lateral ethmoid and frontal. lateral ethmoid-frontal joint is paired.
Joint that articulates the prootic and pterosphenoid. prootic-pterosphenoid joint is paired.
Joint that articulates the prootic and exoccipital. Prootic-exoccipital joint is paired.
Joint that articulates the basioccipital and exoccipital. Basioccipital-exoccipital joint is paired.
Fossa located on the neurocranium that is formed from portions of the sphenotic, frontal and pterotic bones.
Dilatator fossa is present in some characiform fishes.
Joint between the right and left coracoid bones of the pectoral girdle.
Parapophysis that is the lateral projection from the sixth centrum.
Parapophysis that is the lateral projection from the fifth centrum.
Process that arises and projects posterolaterally from parapophysis 4. Posterior limb of parapophysis 4 is bilaterally paired.
Process that arises and projects anterolaterally from parapophysis 4. Anterior limb of parapophysis 4 is bilaterally paired.
Epithelial cell that produces a chemical that triggers antipredator behavior.
replace with CL_0007021 once cl is released.
Chemical substance that functions as an alarm signal.
Fine ridge on surface of scale, often parallel to the circumference of scale.
Shallow area that exists on the prootic.
Dermal bone that is located on or subjacent to the surface anywhere on the body and that is not part of the general complement of scales, dermal bone of the dermatocranium, postcranial axial skeleton or paired fin skeleton. Bony plate may exist singly, or as unpaired or paired clusters or series.
Joint between the centra, and sometimes the neural arches or parapophyses.
Joint between the centra, and sometimes the neural arches or parapophyses of vertebra 6 and vertebra 7.
Anatomical space that is the external opening of a gill slit connecting the pharyngeal cavity to the exterior. Gill opening is usually paired and located on the lateral or ventral surfaces of the head.
In teleosts, there is typically a single gill opening posterior to the operculum.
Centrum that is the fusion of centra 2-4.
Vertebra that is positioned between the vertebra immediately anterior to the first dorsal-fin pterygiophore to the anteriormost vertebra.
Caudal fin lepidotrichium that is distally branched.
Anatomical cluster that consists of more than one type of nuchal plate in an individual.
Uroneural that is the anteriormost element of the uroneural series.
A vertebral centrum that is immediately posterior to preural vertebra 1. Ural centrum 1 is an unpaired median bone.
Ural centrum 1 (polyural terminology) may articulate or fuse with its neural arch dorsally or the neural arch may be absent and with hypural 1 ventrally. Ural centrum 1 may be defined also as the first ural centrum bearing hypurals 1 and 2 (diural terminology).
Opening in the neurocranium to allow communication between the swimbladder and the inner ear.
Anatomical cluster including hypural 3 and more dorsal hypurals that supports the dorsal series of principal caudal lepidotrichia or rays. The upper hypural set articulates or fuses to ural centra 3, 4 or 5 (polyural terminology) or ural centrum 2 (diural terminology) depending on the teleost subgroup. The upper hypural set is composed of unpaired median bones.
The number of hypurals included in the upper hypural set differs among teleostean subgroups. In basal teleosts this may include hypurals 3 to 9 or 10, whereas in more advanced groups this many include hypurals 3 to 5 or even less.
Anatomical cluster including hypurals 1 and 2 that supports part of the ventral principal caudal lepidotrichia or rays and that separates from the dorsal hypural set through the hypural diastema. The lower hypural set articulates or fuses to ural centra 1 and 2 (polyural terminology) or ural centrum 1 (diural terminology) depending on the teleost subgroup. The lower hypural set is composed of unpaired median bones.
Process that is cartilaginous and arises from the distal margin or tip of posterior process of basipterygium and projects posteriorly.
distal cartilage of posterior process of basipterygium
Process that is bony and arises from anteromedial corner of basipterygium and projects anteriorly or anteromedially.
mesial anterior process of basipterygium
internal anterior process of basipterygium
Process that is cartilaginous and arises from the distal tip of internal anterior process of basipterygium.
distal cartilage of internal anterior process of basipterygium
Process that is bony and arises from anterior margin of basipterygium between internal anterior process of basipterygium and external anterior process of basipterygium. Middle anterior process of basipterygium projects anteriorly or anteromedially.
middle anterior process of basipterygium
Process that is cartilaginous and arises from the distal tip of middle anterior process of basipterygium.
distal cartilage of middle anterior process of basipterygium
Process that is bony and arises from anterolateral corner of basipterygium and projects anteriorly or anteromedially.
lateral anterior process of basipterygium
external anterior process of basipterygium
Process that is cartilaginous and arises from the distal tip of external anterior process of basipterygium.
distal cartilage of external anterior process of basipterygium
Process that is bony and arises from lateral margin of basipterygium lateral to pelvic fin lepidotrichium 1 and projects laterally or anterolaterally.
Bone that is attached or adjacent to lateral margin of basipterygium and anterior to pelvic fin lepidotrichium 1. The lateropterygium is a paired bone.
The lateropterygium is present only in a few teleostean subgroups, e.g., some siluriforms.
Perichondrally ossified bone that results from the fusion of two or more hypurals and support a variable number of principal caudal lepidotrichia. The hypural plate is an unpaired median bone.
Larval stage in some teleosts before metomorphosis.
Process that is a ventral projection from the supraoccipital that extends between the exoccipitals to the dorsal margin of the foramen magnum.
Fulcrum that is large, laterally expanded, paired or unpaired, scale-like, and that precedes the base of a fin. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235
Basal fulcra may precede the median fins or both of the paired and median fins. Basal fulcra may be lanceolate, leaf-like or arrow-like in shape. The series of basal fulcra may be formed by unpaired plus paired elements depending on the fish group. Most teleosts lack basal fulcra. For additional information on basal fulcra see Arratia (2008, 2009).
Fulcrum that is a small, paired dermal structure associated with the marginal, leading rays of paired and/or unpaired fins. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235.
Postero-dorsal process of preural vertebra 1 or postero-dorsal process of the compound terminal centrum. The pleurostyle is a paired membrane bone.
The pleurostyle is currently interpreted as a modified pair of uroneurals that fuse to preural vertebra 1 or compound centrum early in ontogeny. However, it is unclear which pair of the series of uroneurals forms the pleurostyle in different teleost subgroups.
A vertebral centrum that is posterior to preural vertebra 1 and consequently the most posterior vertebral centra. Ural centrum is a unpaired median bone.
A ural centrum may be formed by a chordacentrum alone, or chordacentrum plus autocentrum or autocentrum alone depending on the teleost subgroup. An ural centrum may articulate or fuse with its neural arch dorsally or the neural arch my be absent and with a hypural ventrally. The term ural centrum was proposed by Nybelin (1963). For the composition and formation of caudal vertebrae and centra see Arratia (1991), Arratia and Schultze (1992) and Arratia et al. (2001).
Anatomical cluster consisting of only a bony element or a combination of a bony element and one or more scales, or only modified scales, which lies in a fin fold at the base of the uppermost ray.
Pectoral axillary process is an elongate structure formed by one or more additional postcleithra or modified scales or a combination of both, that is firmly attached to a skin fold above the articular condyle of the uppermost pectoral fin ray or lepidotrichium 1.
For additional information see Arratia (1997).
A small bone articulating distally with the haemal arch or a short haemal spine.
Dermal bone located on the ventral surface of the skull and positioned between the two rami of the lower jaw. Anteriorly the gular attaches to the symphysis of the lower jaw through fibrous connective tissue. The gular is an unpaired median bone.
A gular plate is absent in most extant teleosts.
Definition from Johnson and Patterson 1993.
Median chondrified cartilage bound to premaxillary ascending process by a rostro-premaxilla ligament.
Dorsal fin pterygiophore that is the anteriormost pterygiophore of the dorsal fin.
Anatomical cluster that consists of more than one bony plate in an individual.
Anatomical cluster that consists of more than one sensory canal pore.
Anatomical cluster that consists of more than one lateral line scale.
Anatomical cluster that consists of the branchiostegal rays within an individual.
Anatomical cluster that consists of the epibranchial elements within an individual.
Anatomical cluster that consists of the ceratobranchial elements within an individual.
Anatomical structure located in the hindbrain that receives primary electroreceptor input.
Definition reference: McNamara, AM., JP Denizot, CD Hopkins. 2005. Comparative Anatomy of the Electrosensory Lateral Line Lobe of Mormyrids: The Mystery of the Missing Map in the Genus Stomatorhinus (Family: Mormyridae). Brain, Behavior and Evolution 65:188-201.
Anatomical structure that is a subdivision of the cerebellum; it is the location of some lateral line nerve synapses.
Definition based on Albert,2001 [Albert JS. 2001. Species Diversity and Phylogenetic systematics of American Knifefishes (Gymnotiformes, Teleostei). Miscellaneous Publications, Museum of Zoology, University of Michigan no. 190:140 pages.]
Anatomical structure that consists of two neuron types: pacemaker cells and relay cells. The medullary command nucleus commands the timing of the electric organ discharge.
Definition reference: Moortgat, KT, Bullock, TH, and Sejnowski TJ. 2000. J Neurophysiol 83: 971-983. Precision of the Pacemaker Nucleus in a Weakly Electric Fish: Network Versus Cellular Influences.
Multi-tissue structure that is a transient outgrowth of tissue on skin brooding fish that acts as an attachment site for embryos.
Definition reference: James Wetzel, John P. Wourms and John Friel 1997. Comparative morphology of cotylephores in Platystacus and Solenostomus: modifications of the integument for egg attachment in skin-brooding fishes. Environmental Biology of Fishes. Volume 50, Number 1 / September, 1997. Pages 13 - 25.
Erosion channel that radiates out from the growth center (focus) of the scale across and through the circuli.
A demarcation on the scale signfiyning the initial growth point. Requires further classification see Lagler 1947.
Scale that forms part of the posterior border of the caudal-fin organ. Pouch scales are usually hypertrophied.
Definition reference: Weitzman SH, Menezes NA. 1998. Relationships of the tribes and genera of the Glandulocaudiinae (Ostariophysi: Characiformes: Characidae), with a description of a new genus. In: Malabarba LR, Reis RE, Vari RP, Lucena ZMS, Lucena CAS, editors. Phylogeny and Classification of Neotropical Fishes. Porto Alegre: EDIPUCRS. p 171-192.
Surface structure that is a small protuberance on the surface of the body. Nuptial tubercles primarily function to facilitate contact between individuals for breeding.
Nuptial tubercles may be keratinized or nonkeratinized. Also may function in territorial defense or stimulation of females in breeding. Definition reference: Wiley, M. L. and B. B. Collette. 1970. Breeding tubercles and contact organs in fishes: Their occurrence, structure, and significance. Bull Am Mus Nat Hist 143: 143-216.
Organ that consists of a pouch located on the ventral caudal-fin lobe, opening posteriorly, and composed of glandular tissue. The caudal-fin organ presumably functions to secrete pheromones during courtship.
Anatomical cluster that consists of thickened caudal-fin rays modified into a pumping mechanism associated with the caudal-fin organ.
Caudal fin rays can vary in thickness and form of the pump can vary from a simple open groove to complex chambered structure. Definition reference: Weitzman SH, Menezes NA. 1998. Relationships of the tribes and genera of the Glandulocaudiinae (Ostariophysi: Characiformes: Characidae), with a description of a new genus. In: Malabarba LR, Reis RE, Vari RP, Lucena ZMS, Lucena CAS, editors. Phylogeny and Classification of Neotropical Fishes. Porto Alegre: EDIPUCRS. p 171-192.
Intermuscular bone that is located in the dorsal and ventral forward flexures of the myoseptum.
Definition reference: Patterson, C., Johnson, G.D. 1995. The intermuscular bones and ligaments of teleostean fishes. Smithosonian Contributions to Zoology 559:1-85.
Multi-tissue structure that is a cartilaginous or collagenous bar supporting the caudal appendage.
Definition reference: Albert, JS and WL Fink. 2007. PHYLOGENETIC RELATIONSHIPS OF FOSSIL NEOTROPICAL ELECTRIC FISHES (OSTEICHTHYES: GYMNOTIFORMES) FROM THE UPPER MIOCENE OF BOLIVIA . Journal of Vertebrate Paleontology 27(1):17-25
Multi-tissue structure that is region of the body posterior to the last anal-fin ray.
Comments: This is a gymnotiform structure. The caudal appendage can include vertebrae, a cartilginous rod, pterygiophores, anal-fin rays, and intermuscular bones. Definition reference: Albert, JS and WL Fink. 2007. PHYLOGENETIC RELATIONSHIPS OF FOSSIL NEOTROPICAL ELECTRIC FISHES (OSTEICHTHYES: GYMNOTIFORMES) FROM THE UPPER MIOCENE OF BOLIVIA. Journal of Vertebrate Paleontology 27(1):17-25.
Anatomical structure that consists of a sheet of connective tissue attached to the vertebral column and dividing the epaxial and hypaxial musculature.
Surface structure that is a midsaggital strap of flattened ectodermal tissue extending along the posterodorsal midline.
Dorsal organ is a structure found in apteronotid gymnotiform fishes. Definition reference: Albert, JS and WL Fink. 2007. Phylogenetic relationships of fossil neotropical electric fish (Osteichthyes: Gymnotiformes) from the Upper Miocene of Bolivia. Journal of Vertebrate Paleontology 27:17-25.
Ligament that is in the eye and is located at the angle between the cornea and the iris.
CNS white matter, an axonal tract between ventral diencephalon and ventral telencephalon. At 3 d, the anterior catecholaminergic tract includes noradrenergic projections from the hindbrain and dopaminergic projections from ventral dopaminergic neurons. During later development, other catecholaminergic projections may also contribute to the anterior catecholaminergic tract.
Portion of tissue that forms from the swim bladder epithelium at the anterior end of the swim bladder.
Vertebra that is posteriorly adjacent to vertebra 8.
Vertebra that is posteriorly adjacent to vertebra 9.
Vertebra that is posteriorly adjacent to vertebra 10.
Vertebra that is posteriorly adjacent to vertebra 11. May have hemal arch and rib.
Anatomical space which is located beneath the operculum and external to the gills.
Compound endochdondral and dermal bone that results from the fusion of the dermal dermopalatine and the endochondral autopalatine and forms the antero-lateral region of the palate. Commonly, it articulates with the maxilla antero-laterally and with the ethmoidal region medially. The palatine is paired.
Depending on the teleostean group, the palatine may articulate with the entopterygoid posteriorly. The term palatine is usually used for the more advanced teleosts with a large autopalatine and a small dermopalatine represented by a few teeth.
Basal fulcrum that precedes a caudal fin lobe. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235.
Caudal basal fulcra precede the bases of both lobes of the caudal fin or only the dorsal one in basal teleosts. Most teleosts lack basal fulcra on the caudal fin. For additional information on basal fulcra see Arratia (2008, 2009).
A vertebral centrum that is located immediately posterior to ural centrum 2 (polyural terminology). Ural centrum 3 articulates with hypural 3 ventrally. Ural centrum 3 is an unpaired median bone.
Ural centrum 3 lacks a neural arch in teleosts.
A vertebral centrum that is located immediately posterior to ural centrum 3 (polyural terminology) and may fuse to ural centrum 3 early in ontogeny. Ural centrum 4 articulates with hypural 4 ventrally. Ural centrum 4 is an unpaired median bone.
Ural centrum 4 lacks a neural arch in teleosts.
Vertebra that is incomplete or rudimentary and may bear a rudimentary neural arch and sometimes a rudimentary spine or the neural arch and spine are completely absent. Ural vertebrae are one of the last bony elements of the vertebral column, usually smaller than the preural centra. Ural vertebrae are numbered beginning from anterior (1) to posterior (2, 3, 4, etc.). Ural vertebra is an unpaired median bone.
Ural vertebra that is located directly posterior to preural centrum 1. It may bear a rudimentary neural arch and sometimes a rudimentary spine or the neural arch and spine are completely absent and it may articulate or fuse with hypural 1 (polyural terminology). Ural vertebra 1 is an unpaired median bone.
Ural vertebrae 1 may be defined also as the first ural vertebrae bearing hypurals 1 and 2 (diural terminology).
Anatomical cluster including all segmented-and-branched rays plus one unbranched but segmented ray located at the leading margin in each lobe of the caudal fin (Hubbs and Lagler, 1947) and that associates with endoskeletal elements such as hypurals and hemal spines of preural centra 1 and 2 (Arratia, 2008). Caudal principal rays are counted from the dorsalmost one ventrally. Caudal principal rays are unpaired median bones.
In basal teleosts the number of caudal principal rays is about 20. A decreasing of the number of the branched-and segmented rays is observed in more advanced teleosts (see Schultze and Arratia, 1989; Arratia, 1991, 2008). The presence of marginal principal caudal rays as long or longer than the branched-and-segmented principal rays is a synapomorphy of teleosts (Arratia, 2008, 2009).
An anatomical cluster of short rays, shorter than the principal ones, which form the anterior dorsal and ventral series of lepidotrichia of the caudal fin that may be associated with neural spines, epurals and uroneurals (dorsal series) and haemal spines of preural vertebrae (ventral series) (Arratia, 2008). The anteriormost procurrent rays are commonly unsegmented, but the posteriormost ones are usually segmented. The procurrent rays are numbered from caudal to rostral direction. The caudal procurrent ray series is an unpaired median series.
An elongate lateral process ventrally placed to the proximal region of the pleurostyle. The pseudourostyle is paired.
The pseudourostyle occurs only in certain teleost subgroups. It may be well developed in certain characiforms.
Modified neural arch, probably of ural centrum 4, formed by a bony base that may extend along the dorso-lateral surfaces of ural centra and preural centra 1 or 2 and by a well-developed antero-dorsal membranous projection that extends lateral to the base of epural(s) and anterior toward the neural arches and/or spines of preural centra 1 or 2 (Arratia and Schultze, 1992). The stegural is a paired bone.
It is unclear if the structure named stegural is homologous among teleost subgroups.
Urostyle that is the result of fusion of preural centrum 1 with ural centra 1 and 2.
preural centrum 1 + ural centrum 1 + ural centrum 2
Hindbrain nucleus which consists of cell bodies whose axons exit the hindbrain via cranial nerve VIII and innervate hair cells of the lateral line and inner ear. The neurons of these nuclei are unusual in that they extend both contra- and ipsilateral dendrites.
rostral cranial nerve VIII motor nucleus
Telencephalic nucleus which has migrated away from the ependyma and consists of the central, lateral nuclei and the dorsal and ventral entopeduncular nuclei. From Neuroanatomy of the Zebrafish Brain.
obsolete peripheral nucleus of ventral telencephalon
Peripheral nucleus of the ventral telencephalon which is located immediately lateral to the dorsal nucleus of the ventral telencephalon. From Neuroanatomy of the Zebrafish Brain.
area ventralis telencephali, nucleus centralis
obsolete central nucleus of ventral telencephalon
Portion of tissue that consists of afferent axons from the inferior olive and synapsing with Purkinje cells within the molecular layer of the valvula cerebelli and corpus cerebelli.
Motor nucleus of vagal nerve that is located within the dorsolateral portion of rhomobomere 8.
dorsolateral motor nucleus of vagal nerve
Portion of tissue that grows in from the dorsolateral wall of the otic vesicle, forming a dorsolateral partition between the developing anterior and posterior semicircular canals.
Portion of tissue that is a thickening and reshaping of the epidermal basal stratum cells beneath which fibroblasts accumulate to form the scale primordium.
CNS white matter that crosses the midline within the hindbrain.
Head muscle that originates on the anterior region of the cleithrum and inserts on the urohyal. The hypobranchial forms initially as left and right parts that later fuse together forming a cone shape.
Diencephalic nucleus which is located between the dorsal hypothalamus and the caudal tuberal nucleus and does not contain tyrosine hydroxylase immunoreactive cells.
Range covers Schwann cell precursor and immature Schwann cell, should be split and put into CL.
Peripheral nucleus of the ventral telencephalon that has migrated to the periphery of the brain. From Neuroanatomy of the Zebrafish Brain.
area ventralis telencephali, nucleus lateralis
obsolete lateral nucleus of ventral telencephalon
Podocyte that is part of the kidney (mesonephros).
Portion of cranial nerve II where large fasicles of axons from the optic fiber layer come together prior to leaving the eye.
removed axiom: part_of some 'cranial nerve II'
obsolete periventricular nucleus of ventral telencephalon
Diencephalic nucleus which is located in the caudal tuberculum. The preglomerular nuclei make up most of the migrated nuclei within the caudal tuberculum. From Neuroanatomy of the Zebrafish Brain.
presumptive cardiac ventricle primitive heart tube
Podocyte that is part of the pronephros.
Lateral line canal that that crosses the supratemporal region posterior to the openings of the endolymphatic ducts and connects the lateral canals of each side.
Not clear what the taxon constraints are here. The cited reference discusses two species of dogfish.
Organism subdivision that is the side of the body possessing eyes.
Organism subdivision that is the side of the body lacking eyes.
Joint that articulates the premaxilla and maxilla. Premaxillary-maxillary joint is paired.
Pharyngeal arch cartilage located between uncinate process of epibranchial 1 and pharyngobranchial 2.
An interarcual cartilage is present in percomorph fishes (Johnson and Patterson 1993).
Scale that possesses cteni (discrete spines).
Ctenoid scale with two or three alternating rows of cteni marginally and truncated cteni submarginally. (Roberts 1993).
Neuromast of the supraorbital sensory canal in the nasal bone. It is innervated by the buccal nerve rather than by the supraorbital nerve, which invariably innervates neuromasts of the supraorbital canal. (Johnson and Patterson 1993).
Fin that is an unpaired fin located in the sagittal plane of the organism.
pectoral fin distal radial 1 element that is composed of bone tissue.
pectoral fin distal radial 2 element that is composed of bone tissue.
pectoral fin distal radial 3 element that is composed of bone tissue.
Joint that articulates the preopercle and opercle. Preopercle-opercle joint is paired.
Surface structure that is a visible mark on the body resulting from pigmentation.
Scale that is smooth-edged, round or oval and composed of acellular dermal bone lacking small spines on the posterior exposed edge. (from http://www.briancoad.com/Dictionary/introduction.htm).
Typical of many teleosts. Some cycloid scales may have a serrated margin and are then termed spinoid scales. (from http://www.briancoad.com/Dictionary/introduction.htm).
Clear ocular fluid in the anterior segment of the eye. It is produced primarily by dorsal ciliary epithelial cells.
Multi-tissue structure that composes the opaque fibrous outer layer of the eye.
Portion of organism substance that is a gelatinous extracellular matrix structure that fills the vitreous cavity of the eye.
Dermal bone that is typically associated with a fin. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235.
Basal fulcrum that is positioned at the dorsal or anterodorsal margin of the caudal fin. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235.
Basal fulcrum that is positioned at the anteroventral margin of the caudal fin. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235.
Dermal bone that is an unpaired, scale-like structure. Arratia, G. 2009. Identifying patterns of diversity of the actinopterygian fulcra. Acta Zoologica (Stockholm) 90 (Suppl. 1): 220-235.
temporarily relabeled 'fish scute' to distinguish from reptilian scute class. To DO: reconcile definitions for the two sets of classes.
The mesencephalic veins (MsV) enter the mid cerebral veins (MCeV) at the dorsal midline. THe MCeVs originate at the dorsal midline, proceede lateraly in a ventral direction to drain into the paired primordial midbrain channels (PHBC). ogai et al. 2001., Kimmel et al. 1993
A vascular loop attached to the efferent part of the mandibular arch that forms at 3.5 dpf. Isogai et al. 2001.
The branch of the afferent branchial artery that continues posteriodorsally. Isogai et al. 2001.
concurrent branch afferent branchial artery
The anterioventral proceeding branch of the afferent branchial artery. Isogai et al. 2001.
recurrent branch afferent branchial arteries
recurrent branch afferent branchial artery
The vessel between the anterior cerebral vein and the mid cerebral vein. Isogai et al. 2001.
Arteries that irrigate the forebrain and midbrain Isogai et al. 2001.
Extend upward from the PCS, branch to provide an arterial feed to the hindbrain, then drain back down into the PHBC Isogai et al. 2001.
The opercular artery arises from the hyoid stump on the first aortic arch, then follows the lateral margin of the operculum (gill covering) ventrally to reconnect into the proximal part of the first aortic arch. Isogai et al. 2001.
Trunk vessel that connects to the primitive hindbrain channel and the basilar artery at the caudal end of the medulla oblongata. Isogai et al. 2001.
Main route for venous drainage of the anterior and mid cerebral veins as well as portions of the primordial hindbrain channel. Isogai et al. 2001.
Vein that drains the dorsal longitudinal vessel and the caudal portions of the venous capillary network of the medulla oblongata. Isogai et al. 2001.
Hematopoietic tissue derived from the cephalic mesoderm. Predominantly produces myeloid cells. de Jong and Zon 2005.
Vessel that connects to the primitive hindbrain channel and the basilar artery at the caudal end of the medulla oblongata. Isogai et al. 2001.
Vein that connects to the hyaloid vein that drains the eye. External to eye. Isogai et al. 2001.
Vessels run longitudinally along the horizontal myoseptum. These vessels are not functional until after lumenization which occurs near 4 dpf. Isogai et al. 2003.
A continuation of the anterior mesenteric artery, which branches out from the dorsal aorta just caudal to the pronephric glomus. Isogai et al. 2001.
The artery that carries blood to the eye. It branches from the internal carotid artery and enters the eye ventrally through the optic fissure. Isogai et al. 2001.
Vessel that branches from cranial division of the internal carotid artery, extending laterally around the rostral end of the head. Isogai et al. 2001.
After the primitive prosencephalic artery forms it becomes disconnected from the cranial division of the internal carotid artery and instead it connects to the anterior mesencephalic central artery and the communicating vessels of the palatocerebral artery.
The PLA branches ventrally from the CrDI. It extends rostrally along the base of mid- and forebrain, then loops medially and links to the corresponding vessel from the other side of the embryo. Isogai et al. 2001.
Connect the palatocerebral artery with the prosencephalic artery. Isogai et al. 2001.
communicating vessel palatocerebral artery
Arteries that irrigate rostral regions of the midbrain. They extend between the Basial communicating artery to the anterior cerebral vein. Isogai et al. 2001.
Drains the PLA loop proceeds straight caudally along the cranial midline just above the pharynx, just below the diencephalon. Forms a 'T' with the palatocerebral veins. Isogai et al. 2001.
Vein that drains the median palatocerebral vein into the optic vein. Isogai et al. 2001.
Composed of scattered layers of interrupted elastic lamina. Hu et al. 2001.
Composed of 7-10 layers of helically arranged smooth muscle cells surrounded by a fine network of collagen, reticular, and elastic fibrils. Hu et al. 2001.
Composed of subendothelium with longitudinally oriented collagen, reticular fibrils, elastic fibers, and smooth muscle cells bound by a thin endothelial layer. Hu et al. 2001.
Cardiac conduction system, characterized by slow impulse propagation and prolonged refractory periods.
Portion of the cardiac conduction system, with rapid impulse propagation.
Project rostrally and dorsally from the AMCtA to to irrigate the midportion of the midbrain Isogai et al. 2001.
Project dorsally from BCA to irrigate the caudal part of midbrain Isogai et al. 2001.
Unpaired artery departing from dorsal aorta, typically supplying the small intestine
These arteies branch dorsally from both sides of the posterior communicating artery looping up to join with the opposite MtA as well as with both middle cerebral veins at the dorsal midline of the head. Isogai et al. 2001.
The nasal arteries start at the internal carotid artey and travel rostrally, passing along the right and left walls of the nasal sac at the most rostral end of the head. From the nasal sac, the NA flows into the nasal veins. Isogai et al. 2001.
Unpaired artery departing from dorsal aorta that typically supplies the large intestine
An elaborate set of vessels that branche off caudally from the anterior mesenteric artery just after the dorsal aorta. The SBA vascular loops are located on the ventral side of the swim bladder. Isogai et al. 2001.
Positioned in the intraray mesenchym between the hemirays of the lepidotrichia,. Huang et al. 2003.
Lie flanking and just lateral to the fin ray, in the interray mesenchyme. Huang et al. 2003.
Vessels that travel between artery and veins or vein and vein in a single ray.
Vessels that travel between veins in adjacent rays.
Neuromast that is part of the dorsal lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)
Primordium that forms the first neuromasts of the posterior lateral line. This primordium travels at 1.5-1.7 somites/hour and deposits neuromast that are polarized along the antero-posterior axis.
primary posterior lateral line primordia
primary posterior lateral line primordium
Second lateral line primordium. These primordia moves at 0.2 somites/hour and deposite neromasts that are polarized in a dorso-ventral direction.
secondary posterior lateral line primordia
secondary posterior lateral line primordium
A migrating group of cells originating from an anterior lateral line placode. The primordium deposits neuromasts and interneuromasts between them during its migration.
A migrating group of cells originating from the middle lateral line placode. The primordium deposits neuromasts with interneuromasts between them.
A surface structure that will eventually grow to form a barbel. The primordium is rich in taste buds. The final location for taste buds present in the primordium is the distal tip of the mature barbel.
Intestinal epithelium which lines the lumen of the intestinal bulb.
Epithelium that surrounds a primary tooth. This epithelium is committed to formation of replacement teeth.
A branch of the 8th cranial nerve that innervates the cristae ampullaris.
Part of regeneration epithelium at the tip of the fin/limb [ZFA,modified].
distal epidermal cap of regenerating fin/limb
Layer of the wound epidermis that surrounds the blastema in the fin or limb[ZFA,modified].
basal regeneration epithelium of regenerating fin/limb
Iridescent iridophore containing gold reflecting platelets.
Iridescent iridophore containing silver reflecting platelets.
Bile duct that collects from the intrahepatic ducts and feeds into the common bile duct.
Portion of the liver which develops on the fish's ventral side.
An interneuron in the spinal cord. CoPA are bipolar with 'T' shaped dorsal dendrites, have contralateral longitudinal axons that crosses the cord dorsal to the Mauthner neuron and ascends in the dorsal cord.
This term entered TAO as a leaf node in the zebrafish AO and is not in the CL. incorrectly generalized to teleosts
An interneuron of the spinal cord. CoSA, have contralateral longitudinal axons that crosses the cord dorsal to the Mauthner neuron and ascends in the dorsal cord.
This term entered TAO as a leaf node in the zebrafish AO and is not in the CL. obsoleting because incorrectly generalized to teleosts.
This term entered TAO as a leaf node in the zebrafish AO and is not in the CL. incorrectly generalized to teleosts so being obsoleted.
This term entered TAO as a leaf node in the zebrafish AO and is not in the CL.
middle dorsal 2 contralateral llf interneuron
middle dorsal 2 contralateral mlf interneuron
A bifurcate interneuron. It is a commissural neuron with both ascending and descending axons in the ventrolateral cord contralateral to its cell body.
This term entered TAO as a leaf node in the zebrafish AO and is not in the CL. This may be the same as CoBL. incorrectly generalized to teleosts so being obsoleted.
rostral intermediate 2 caudal interneuron
rostral intermediate 2 rostral interneuron
May have 12 neurons in each hemi rhombomere ZDB-PUB-060217-9 7 neurons in each hemi rhombomere 080227-17 and 931014-770
middle dorsal 3 contralateral llf interneuron
middle dorsal 3 contralateral mlf interneuron
CNS interneurons located in the midbrain.
mesencephalon lateral rostral interneuron
mesencephalon lateral caudal interneuron
mesencephalon lateral medial interneuron
Hindbrain interneuron that is part of rhombomere 7, with 2 ventral neurons in each hemi-rhombomere.
Cranial vasculature where the posterior cerebral veins and the trans-choroid plexus branch form a circuit around the 4th ventricle choroid plexus.
median fin radial element that is composed of bone tissue.
median fin proximal radial element that is composed of bone tissue.
Lepidotrichium that is articulated or segmented, and that can be simple or branched.
A bifurcate interneuron where the axon projects ventrally, crossing the spinal cord ventral to the Mauthner axons before bifurcating and extending dorsally.
incorrectly generalized to teleosts so being obsoleted.
multipolar commissural descending interneuron
A interneuron of the spinal cord with an ipsilateral axon that extends ventral to the Mauthner axon then turns dorsally and caudally and sometimes has a minor ascending branch.
A spinal interneuron with a dorsal dendrite that extends caudally. CoLA also has midlateral process that extend rostrally and caudally, the axon crosses the cord dorsal to the Mauthner cell and ascends, extending dorsally. Axon has minor descending branch.
commissural longitudinal ascending interneuron
unipolar commissural descending interneuron
replaced by CL_0007022 once cl is released.
Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons.
obsolete polychromatophilic erythroblast
obsolete auditory epithelial support cell
Fibrous joint connecting the parietal bones.
Is a fibroblast that differentiates from the de-differentiated cells of the blastema.
Interneurons of the spinal cord that arise from the V1 proliferation domain. The CiA neurons inhibit motoneurons, other ventral interneurons and also inhibit dorsal sensory neurons involved in sensory gating,. CiA have ipsilateral axonal projections in both motor and sensory regions of spinal cord.
incorrectly generalized to teleosts/vertebrates.
A portion of tissue formed between the base of the intestinal villi that is part of the intestinal epithelium where intestinal stem cells are located. In the intestine no crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips.
Capillary that has endothelial cells that provide an uninterrupted lining, and only allow small molecules, like water and ions to diffuse through tight junctions which leave gaps of unjoined membrane which are called intercellular clefts.
Blood vessel endothelium that has tight junctions between the endothelial cells[ZFA].
Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse
the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences
Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA].
Synovial joint that articulates the hyomandibula and the opercle.
Fossa on the pterotic where the hyomandibula articulates.
Muscle that moves parts of the body in a superior direction to an erect position. Antagonistic to depressor muscle.
Joint that articulates the posterior edge of the preopercle horizontal limb with the symplectic.
In ZFA, is a type of fibrous joint. May need to stay more general in TAO.
preopercle horizontal limb-symplectic joint
Space enclosed by the trabeculae cranii. The anterior tip of the notochord extends into the posterior region of the hypophyseal fenestra.
A muscle that moves body parts into an inferior direction or lowered position. Antagonistic to erector muscle.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary. During gonadal development, the gonad may be transiently intersexual where there is a parallel presence of both oocytes and spermatocytes.
A thin layer of smooth muscle immediately beneath the base of the villi which permits the intestinal mucosa to dynamically move and fold.
Foramen in the hyomandibula that allows passage of the anterior lateral line nerve and the facial nerve (cranial nerve VII).
Joint that articulates the anterior edge of the preopercle vertical limb and the hyomandibula.
preopercle vertical limb-hyomandibula joint
Smooth muscle of the enteric muscle system in which the cells are aligned perpendicular to the lumen of the gut.
Portion of the renal tubule which is just posterior to the distal early tubule.
Simple squamous epithelium that lines the capsule of the pronephric glomerulus.
pronephric glomerular capsule epithelium
Fin fold of the pectoral fin bud, resulting from mesenchyme migration into the apical fold.
The functional webs of the paired fins. They arise as a consequence of apical fold (AER) expansion and of migration of the distal mesenchyme. The fin folds are delimited by a dorsal and a ventral striated epidermis. The cells of the epidermal basal stratum are positioned on a basement membrane. Directly beneath the basement membrane of each side there is an array of actinotrichs, fibers of the extracellular matrix which act as supportive elements of the larval fin folds.
Ionocyte located in the integument during embryonic and larval stages.
Integument ionocyte rich in Na,K-ATPase.
Integument ionocyte rich in vacuolar-type H+ ATPase and carbonic anhydrase
Posterior protrusion of the third ventricle.
posterior recess of diencephalic ventricle
medial longitudinal catecholaminergic tract
CNS white matter, axonal tract interconnecting catecholaminergic cell groups in the posterior tuberculum and hypothalamus.
Portion of the pancreatic duct, external to the pancreas body that connects the pancreas with the hepatopancreatic ampulla.
dorsal fin distal radial 1 element that is composed of bone tissue.
dorsal fin distal radial 2 element that is composed of bone tissue.
dorsal fin distal radial 3 element that is composed of bone tissue.
dorsal fin distal radial 4 element that is composed of bone tissue.
dorsal fin distal radial 5 element that is composed of bone tissue.
dorsal fin distal radial 6 element that is composed of bone tissue.
dorsal fin distal radial 7 element that is composed of bone tissue.
dorsal fin distal radial 8 element that is composed of bone tissue.
dorsal fin proximal radial 3 element that is composed of bone tissue.
dorsal fin proximal radial 4 element that is composed of bone tissue.
dorsal fin proximal radial 5 element that is composed of bone tissue.
dorsal fin proximal radial 6 element that is composed of bone tissue.
dorsal fin proximal radial 7 element that is composed of bone tissue.
dorsal fin proximal radial 8 element that is composed of bone tissue.
The dorsal part of the ear. Comprises the three semicircular canals, which connect to the utricle.
The ventral portion of the ear. It contains the saccule and the laguena which are the primary auditory organs.
Duct that crosses the midline connecting the sacculi.
Early-forming telencephalic neural cluster. Neurons of the dorso-rostral cluster (drc) extend axons to form the supra-optic tract (SOT) and the anterior commissure (AC). Ross et al., 1992.
Early-forming neural cluster located in the rostral diencephalon. At 19 h, axons arising from the vrc grow caudally to pioneer the tract of the postoptic commissure (TPOC). Ross et al., 1992.
Early-forming neural cluster of the ventral midbrain. At 16 h, axons of the vcc grow caudally to pioneer the medial longitudinal fasciculus (MLF), which is part of the larger ventral longitudinal tract (VLT). Later, neurons from this cluster project axons rostrally into the tract of the post-optic commissure (TPOC). Ross et al., 1992.
Early-developing neuronal cluster of the epiphysis. By 24 hpf the pioneer axon of the dorsoventral diencephalic tract (DVDT) has arisen from the ec and grown ventrally. As this axon encounters axons of the TPOC, it makes a near-90 rostral turn and grows rostrally among axons of the TPOC growing in the opposite direction. Ross et al., 1992.
Hemal prezygapophyses are paired, anteromedially directed processes arising from the bases of hemal arches, ligamentously joined to the hemal postzygapophyses of the preceding vertebra. Posterior caudal vertebrae close to the caudal fin lack hemal prezygopophyses.
Part of the forebrain that is ventral to the ventral thalamus and dorsal to the preoptic area. See page 44 of the Atlas of Early Zebrafish Brain Development.
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Is a hyoid muscle that inserts at the most anterior basibranchial and also at the posterior ends of the ceratohyals and functions in jaw closure.
Is a hyoid muscle that attaches to the dorsomedial faces of the hyosymplectics.
anterior pillar of the semicircular canal
pillar of the anterior semicircular canal
ventral piller of the semicircular canal
pillar of the lateral semicircular canal
Rod-like internal median skeletal support elememts of the anal fin, which articulate with the distal radial elements.
Radial elements are the internal skeletal supports of the median and paired fins.
Radial elements may be cartilaginous or bony; always present at the base of fins; typically support lepidotrichia.
Pelvic fin radial elements are internal skeletal supports of the pelvic fin.
Endochondral element that is paired and supports the pelvic fin. The basipterygium has a posteromedial process called the ischiac process (Wietzman 1962).
Rod-like internal median skeletal support elements of the anal fin, which articulate with the lepidotrichia distally.
Rod-like internal median skeletal support elements of the dorsal fin, which articulate with the lepidotrichia distally.
Rod-like internal median skeletal support elements of the dorsal fin, which articulate with the distal radial elements.
Pectoral fin radial elements are the internal skeletal supports of the pectoral fin which develop from the pectoral fin endoskeletal disc, supports the pectoral lepidotrichia or fin rays and connects the lepidotrichia with the primary pectoral girdle.
There are two paired series of pectoral radial elements, the proximal and the distal ones that may have variable shapes and sizes.
Pectoral fin radial element which develops from the pectoral fin endoskeletal disc, supports a few pectoral lepidotrichia or fin rays and connects the lepidotrichia and distal radial elements with the primary pectoral girdle (scapula and coracoid).
Two to four flat or slightly rod-like proximal pectoral radial elements, bilaterally, can be found in teleosts. Pectoral proximal radial elements are commonly hour-glass or rectangular shaped. The presence of four pectoral proximal radial elements is interpreted as a synapomorphy of teleosts (Patterson 1977, Arratia 1999).
Pectoral fin radial element that sometimes ossifies, develops from the pectoral fin endoskeletal disc, and is located at the proximal region of a lepidotrichium, between its hemitrichia. Pectoral fin distal radial element is paired.
A variable number of pectoral distal radial elements may be present in each pectoral fin. They are commonly small elements, rod-like, round or square shaped.
Dorsal fin radial element that is the rod-like internal median skeletal support element of the dorsal fin located between the dorsal fin proximal radial element and dorsal fin distal radial element.
Anal fin radial element that is the rod-like internal median skeletal support element of the anal fin located between the anal fin proximal radial element and anal fin distal radial element.
Anal fin radial elements are internal skeletal supports of the anal fin.
Dorsal fin radial elements are internal skeletal supports of the dorsal fin.
Pectoral fin proximal radial element that is the most anterior or dorsal pectoral fin radial element.
Pectoral fin proximal radial element that is the second most anterior or dorsal pectoral fin radial element.
Pectoral fin proximal radial element that is the third most anterior or dorsal pectoral fin radial element.
Pectoral fin proximal radial element that is the fourth most anterior or dorsal pectoral fin radial element.
Radial element that is part of a median fin.
anal fin proximal radial element that is composed of cartilage tissue.
radial element that is composed of cartilage tissue.
pelvic fin radial element that is composed of cartilage tissue.
basipterygium element that is composed of cartilage tissue.
anal fin distal radial element that is composed of cartilage tissue.
dorsal fin distal radial element that is composed of cartilage tissue.
dorsal fin proximal radial element that is composed of cartilage tissue.
pelvic fin distal radial 2 element that is composed of cartilage tissue.
pelvic fin distal radial 3 element that is composed of cartilage tissue.
pelvic fin distal radial 1 element that is composed of cartilage tissue.
pectoral fin radial element that is composed of cartilage tissue.
pectoral fin proximal radial element that is composed of cartilage tissue.
pectoral fin distal radial element that is composed of cartilage tissue.
dorsal fin middle radial element that is composed of cartilage tissue.
anal fin middle radial element that is composed of cartilage tissue.
anal fin radial element that is composed of cartilage tissue.
dorsal fin radial element that is composed of cartilage tissue.
dorsal fin proximal radial 1 element that is composed of cartilage tissue.
dorsal fin proximal radial 2 element that is composed of cartilage tissue.
pectoral fin proximal radial 1 element that is composed of cartilage tissue.
pectoral fin proximal radial cartilage 1
pectoral fin proximal radial 2 element that is composed of cartilage tissue.
pectoral fin proximal radial cartilage 2
pectoral fin proximal radial 3 element that is composed of cartilage tissue.
pectoral fin proximal radial cartilage 3
pectoral fin proximal radial 4 element that is composed of cartilage tissue.
pectoral fin proximal radial cartilage 4
pectoral fin distal radial 1 element that is composed of cartilage tissue.
pectoral fin distal radial 2 element that is composed of cartilage tissue.
pectoral fin distal radial 3 element that is composed of cartilage tissue.
median fin radial element that is composed of cartilage tissue.
median fin proximal radial element that is composed of cartilage tissue.
dorsal fin distal radial 1 element that is composed of cartilage tissue.
dorsal fin distal radial 2 element that is composed of cartilage tissue.
dorsal fin distal radial 3 element that is composed of cartilage tissue.
dorsal fin distal radial 4 element that is composed of cartilage tissue.
dorsal fin distal radial 5 element that is composed of cartilage tissue.
dorsal fin distal radial 6 element that is composed of cartilage tissue.
dorsal fin distal radial 7 element that is composed of cartilage tissue.
dorsal fin distal radial 8 element that is composed of cartilage tissue.
dorsal fin proximal radial 3 element that is composed of cartilage tissue.
dorsal fin proximal radial 4 element that is composed of cartilage tissue.
dorsal fin proximal radial 5 element that is composed of cartilage tissue.
dorsal fin proximal radial 6 element that is composed of cartilage tissue.
dorsal fin proximal radial 7 element that is composed of cartilage tissue.
dorsal fin proximal radial 8 element that is composed of cartilage tissue.
Paired, cup-shaped cartilage that are dorsal to the septomaxillae and anterior to the oblique cartilage. The anterior, convex face of each alary cartilage is synchondrotically fused to the superior prenasal cartilage and the ventral edge is fused to the superior margin of the crista intermedia.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Dorsal process that extends toward the nasal bone. The posterior (inner) face of each alary process is concave and is invested dorsomedially by the superior prenasal cartilage and ventromedially by the inferior prenasal cartilage.
Foramen for the R. alveolaris of Nerve VII and the alveolar artery.
Point of insertion of the adductor mandibulae musculature.
Process that extends anteriorly from the planum triangulare and invests the medial face of the pars facialis of the maxilla.
Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule.
anterior process of pars palatina of maxilla
In a triradiate pterygoid, the process that extends anteriorly towards the maxilla.
oberste abteilung des zweiten visceralbogens
Process that extends medially from the ventromedial corner of the palatoquadrate cartilage and articulates or fuses to the anterior wall of the otic capsule via the basitrabecular process.
Anatomical structure which forms from an enlargement of the anterior portion of each gonad in all male bufonid larvae and consists of ovarian tissues.
Undifferentiated cell that is produced by early cleavages of the fertilized egg (zygote).
The part of the skull that encloses the brain and surrounds the inner ear.
Narrow process of the skeletal support that projects forward.
obsolete cartilage bridge of nasal skeleton
Lateral cartilaginous border of the fenestra endochoanalis.
Lateral wall of chondrocranial braincase between lamina orbitonasalis and pila metoptica.
Accessory cavity located ventral to the cavum principale and cavum medius.
Small accessory cavity located between the cavum principale and cavum inferius.
The largest part of the nasal cavity, containing the olfactory epithelium.
Anterior-lateral projections from the corpus of the hyoid apparatus.
Thin, horizontal ridge that extends medially from the corpus of the septomaxilla; it lays on the lamina inferior.
Paired, oblique plates of cartilage located ventral to the alary cartilages. The dorsomedial margin of each crista intermedia is fused to the transitional zone between the septum nasi and the tectum nasi, whereas the ventrolateral margin bears two laminae, the lamina superior and the lamina inferior.
Short and blunt process that extends posteriorly from the posteromedial margin of the postnasal wall, on the anterodorsal corner of the orbit above the medial orbitonasal foramen.
Also known as fibrous connective tissue. Forms ligaments and tendons and is characterized by densely packed collagen fibers that have great tensile strength.
Flange that extends ventrally from about the middle portion of the margo mandibularis.
ventral flange of anterior ramus of pterygoid
Large anterior outgrowth of the septomaxilla that is directed into the space between the alary cartilage and the lamina inferior.
Opening on the ventral aspect of the nasal capsule. It contains the apertura nasalis interna.
Opening on the anterolateral aspect of the nasal capsule. It contains the apertura nasalis externa.
Opening on the lateral side of the nasal capsule.
Small opening at the anterior tip of the nasal capsule, on the floor of the cavum inferius. It is located medially to the base of the inferior prenasal cartilage and serves for the passage of the ramus medialis narium and arteria orbitonasalis.
Elongated opening located on the lateral side of the nasal capsule.
Large opening of the nasal floor anterior to the fenestra endochoanalis.
Independent, horizontal bar of cartilage located on the anterior part of the fenestra ovalis in front of the pars interna plectri.
Complex formed by two units, the hyoid and laryngeal apparatuses, which are both derived from the larval hyobranchial skeleton.
Elongate cartilage that extends anteroventrally from the solum nasi to abut the ventral portion of the posterior aspect of the alary process of the premaxilla. It was first described by Wiedersheim in 1876.
Larval lower jaw lies anterior to Meckels cartilage.
Lateral expansion of the crista intermedia that serves as the floor of the cavum medium.
Free, dorsal margin of the lamina inferior.
Lateral expansion of the crista intermedia that serves as the roof of the cavum medium.
Obsolete term in XAO. redundant with stage+skeletal system. Can be properly reinstated if needed.
Ventrally directed margin that connects the anterior and posterior rami of the pterygoid.
Dorsal margin of the maxilla between the frontal and zygomatico-maxillary processes.
Margin that connects the anterior and medial rami of the pterygoid.
Anterior margin of the squamosal that takes part in the formation of the orbit.
Margin that connects the posterior and medial rami of the pterygoid.
A compound bone consisting of maxilla and palatine, can also contain a prefrontal and/or lacrimal; present in adult Gymnophiona.
Opening on the postnasal wall for the medial branch (= ramus medialis nasi) of the ophthalmicus nerve.
In a triradiate pterygoid, the process that extends medially towards the otic capsule.
Anterior projection of the septum nasi that protrudes through the anterior nasal wall.
A compound bone consisting of premaxilla, nasal and sometimes septomaxilla in adult members of Caeciliidae and Typhlonectidae.
Semi-circular cartilaginous sheet that lies lateral to the side of the septum nasi.
Foramen that forms a passage for one of the branches of the trigeminal nerve into the nasal region.
Ossified posterior articular portion of Meckel's cartilage.
A bone that forms both the floor of the braincase and the posterior part of the skull.
Osseous expansion of the posterior and medial rami of the pterygoid.
Ramus (process) that extends medially toward the otic capsule.
Sliver of bone that invest part of or all the posterior aspect of each antorbital plane.
palatine process of pars palatina of premaxilla
palatine process of the pars facialis of the maxilla
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon. Logical definition added by cjm.
Cartilaginous bridge that extends posteriorly to the anterolateral corner of the posterior nasal wall.
connection between lamina nariochoanalis and postnasal wall
Process that extends anteriorly from the orbitotemporal region.
Paired processes extending lateraly from the posterior body of the parasphenoid that, when present, support the otic capsules ventrally.
Paired, elongate, ventrolaterally-orieted cartilaginous structures that extend to the premaxilla-maxilla articulation.
Posterior end of Meckel's cartilage that forms the articular head of the mandibular arch.
Plate-like structure that lies in the fenestra ovalis. It arises within the membrana opercularis in the posterior part of the fenestra.
Lingual ledge on the inner surface of the maxilla.
Lingual ledge on the inner surface of the premaxilla.
Consists of enlarged cistern against which the operculum and footplate of the columella rest in the oval window. Together with the endolymphatic systems comprises the membranous labryinth of the inner ear. Duellman and Trueb 1994.
A strut of cartilage extending dorsally from the basal plate and with other similar cartilages forming the sides of the brain case. The pila antoptica is posterior to pila metoptica together with which it may enclose the foramen for the ocular motor nerve and opthalmica magna artery.
A strut of cartilage extending dorsally from the basal plate and with other similar cartilages forming the sides of the brain case. The pila metoptica is anterior to pila antoptica together with which it may enclose the foramen for the ocular motor nerve and opthalmica magna artery. Anterior to the pila antoptica is the pila preoptica (another pillar of cartilage) between these two cartilages emerges the optic and trochlear nerves.
Vertical plate of cartilage that is fused posterodorsally to the oblique cartilage and anteriorly to the lamina inferior.
Cartilaginous, distal expansion of the lamina orbitonasalis that invests the pars facialis of the maxilla medially.
Complex sound-conducting anatomical structure.
Process that extends posteriorly from the planum triangulare and invests the maxilla laterally and the anterior ramus of the pterygoid medially.
posterior maxillary process dorsal process
In a triradiate pterygoid, the process that extends posterolaterally towards the jaw articulation.
Paired, anteriorly concave structures that form the posterior limit of nasal capsule. It consists of two parts: a ventral piece, the lamina orbitonasalis, and a dorsal plate that is part of the tectum nasi.
Point of insertion of the masticatory musculature.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon. Modified by cjm: added logical definition
preorbital process of the pars facialis of the maxilla
Cartilaginous or ligamentous connection between the pars externa plectri and the crista parotica.
Posterior part of the corpus of the septomaxilla; the posterior surface of the processus infrafenestralis is in contact with the oblique cartilage.
Dorsolateral process of the of the medial ramus of the pterygoid.
Posterior, toothless portion of the maxilla by which it usually comes in contact with the quadratojugal.
Posterior end of the pars palatina of the maxilla that is in contact with the anterior ramus of the pterygoid.
Posterodorsal extension of the maxilla by which it establishes contact with the squamosal.
Compound bone of adult Gymnophiona, consisting of dentary, coronoid and mentomeckelian.
Palatal bones of intramembranous origin that lie anterior to the otic capsules, lateral to the orbits, and medial to the maxillae.
Process that extends anteriorly from the anterolateral margin of the palatoquadrate and articulates or synchondrotically fuses to the posterior end of the posterior maxillary process.
Is a recess on the surface of the premaxilla near to the base of the pars facialis.
Is a space on the interior surface of the pars facialis of the maxilla
Bony process that is part of the articular and is the point of insertion of the m. interhuoideus posterior.
Is a process of the nasal bone directed anteriorly towards the rostrum.
The anterior connective tissue partition between walls of otic capsule around which the membranous semicircular canals pass.
The lateral connective tissue partition between walls of otic capsule around which the membranous semicircular canals pass.
The posterior connective tissue partition between walls of otic capsule around which the membranous semicircular canals pass.
Elevation of the dorsal surface of the solum nasi medial to the fenestra endochoanalis that provides support for the eminentia olfactoria.
skeletal support for eminentia olfactoria
Unpaired, horizontal plate that forms the floor of the nasal capsule.
Endochondral bone that forms the anterior portion of the braincase and forms from one ossification center on each side of the orbital cartilage.
Groove located between the pars dentalis and the bases of the maxillary teeth.
Groove located between the pars dentalis and the bases of the premaxillary teeth.
A groove on the palatoquadrate that is occupied by the Meckel's cartilage.
Paired, elongate cartilages that extend anteroventrally to abut the dorsomedial margin of the posterior face of the alary process of the premaxilla. The function of these cartilages is to transmit the movement of the premaxilla to the alary cartilages during the closure of the apertura nasalis externa.
The suprangular or surangular is a jaw bone found in most land vertebrates, except mammals. It's usually in the back of the jaw, on the upper edge, and is connected to all other jaw bones: dentary, angular, splenial and articular. It is often a muscle attachment site.
Median, unpaired bone that can form the dorsal margin of the foramen magnum.
Endochondral ossification of the dorsomedial portion of the braincase.
Cartilaginous connection between the orbital cartilage and otic capsules.
Roof of the nasal capsule, confluent with lamina orbitonasalis posteriorly and united to septum nasi.
Central, funnel-shaped, ossified portion of the tympanic annulus fused to the squamosal bone.
Longest of the three squamosal rami; it invests the dorsolateral margin of the palatoquadrate. The distal end of the ventral ramus invests the quadrate and articulates with the quadratojugal.
Ramus (process) that projects anteriorly from the dorsal body of the squamosal and forms part of the posterior margin of the orbit.
Skeletal structure that separates the inferior and superior perilymphatic foramina.
Rod-shaped process that extends caudally from the inferior edge of the planum terminale.
Anterior, rounded portion of the corpus of the septomaxilla.
Sharp ridge that extends medially from the basal part of the processus infrafenestralis; it separates the diverticulum proncipale from the diverticulum medium.
Synchondrotic or synostotic connection between the footplate of the pars media plectri and the ventral margin of the fenestra ovalis.
Process that extends anterolaterally toward the maxilla-premaxilla articulation.
Anterio portion of the maxilla that may contact the nasal and take part in the formation of a groove for the nasolacrimal duct.
processus praeorbitalis of the pars facialis
Most anterior part of the maxilla, which is in contact with the premaxilla.
Depression lacated on the inner surface of the maxilla between the palatine process and the pars palatina.
Alternative more fish orientated definition. A fossa that is a depression in the proximal end of the maxilla involved in articulation with the palatine. [Baldwin, CC and Johnson GD. 1996. Interrelationships of Aulopiformes. Pages 355-404 in MLJ Stiassny, LR Parenti, and DG Johnson, (eds.), Interrelationships of fishes. Academic Press, San Diego, CA.]
Portion of the quadratojugal that makes contact dorsally with the distal portion of the squamosal.
Anterior part of the quadratojugal that is in contact with the processus posterior of the maxilla.
Dorsal process of the lamella alaris located at the anterior end of the margo orbitalis; a narrow ligament that runs from the frontoparietal is attached to it.
Posterior process of the lamella alaris.
processus posterodorsalis of lamella alaris
Process that extends laterally from the anterior process; its bifurcation from the postchoanal process occurs at the level of the dentigerous process.
Process that extends laterally from the anterior process; its bifurcation from the prechoanal process occurs at the level of the dentigerous process.
Margin between the prechoanal and postchoanal process. It bounds the fenestra endochoanalis.
Ridge on the dorsal surface of the vomer that runs from the anterior to the postchoanal processes of the vomer; it takes part in the fixation of the bone to the lateral margin of the solum nasi.
Posterior projection of the median part of the parsphenoid, which may extend over the posterior margins of the subotic alae.
Azygous or paired bone that occurs on the ventral surface of the hyoid plate.
Is the space along the anterior edge of the hyoid plate between the hyale and through which passes the hyoglossus muscle as it passes dorsally into the tongue.
Processes that flank the hyales laterally and extend anterolaterally from the anterolateral margin of the hyoid plate. They are formed as a result of new cartilaginous growth lateral to the basibranchial.
Paired processes that extend posterolaterally from the posterolateral margin of the hyoid plate. These processes are formed as a result of new cartilaginous growth lateral to the basibranchial and hypobranchial plate.
Cartilaginous, paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes invest the laryngeal apparatus and are ossified in the adult.
Paired processes that extend posteroventrally from the anterolateral margins of the cricoid ring.
Median process located on the posterior end of the cricoid cartilage.
Depression that houses the hypoglossus nerve and is located between the anterolateral process and the proximal part of the hyale.
Foramen that houses the hypoglossus nerve and is located between the anterolateral process and the proximal part of the hyale.
Strip of cartilage that forms the lateral margin of the foramen nervi hypoglossi.
Anterior end of the arytenoid cartilage.
Posterior (cardiac) end of the arytenoid cartilage.
Paired stalks located dorsolateral to the vertebral centrum that provide support to the lateral margins of the neural arch laminae.
Anterior, single or paired concave facets for articulation with the condyle(s) of the urostyle.
Indentation on the anterior margin of the pedicel. When two vertebrae articulate, the anterior notch of one vertebra and the posterior notch of the other create a bilateral intervertebral space.
Space formed by the anterior and posterior intervertebral notches. The intervertebral spaces accommodate the spinal nerves as they emerge from the spinal canal.
Indentation on the posterior margin of the pedicel. When two vertebrae articulate, the anterior notch of one vertebra and the posterior notch of the other create a bilateral intervertebral space.
Paired processes that represent the rib attachments to the vertebra plus the ribs.
Holochordal vertebral centra that are concave anteriorly and convex posteriorly; they bear a condyle on the posterior end for the articulation with the posterior adjacent vertebral centrum, forming a ball-and-socket joint that allows extensive motion in most directions.
Ectochordal or stegochordal vertebral centra that are convex anteriorly and concave posteriorly; they bear a condyle on the anterior end for the articulation with the posterior adjacent vertebral centrum, forming a ball-and-socket joint that allows extensive motion in most directions.
Vertebral centrum that originates from ossification of the dorsal portion of the perichordal tube; the resulting element tends to be depressed in cross section.
Vertebral centrum that originates from ossification of the entire perichordal tube; the resulting element is cylindrical in cross section and may have an open (notochord retained) or solid center.
Vertebral centrum that bears saddle-shaped articular surfaces at both ends, having a convexity in the right-left axis and a concavity in the dorsoventral axis. This morphology allows great lateral and vertical flexion.
Vertebral centrum with flat ends. Between successive vertebrae there is a fibrocartilaginous intervertebral body with a gel-like core, the nucleus pulposus, which is derived from the embryonic notochord. Acoelous vertebrae seem especially suited to receive and distribute compressive forces within the vertebral column.
Ectochordal, biconcave or terminally flat vertebral centrum. This design seems to allow limited motion in most directions. An intervertebral body (which may or may not be independent from the adjacent centra) fills the cavity between successive centra. The intervertebral body usually is formed by soft material that may be derived, at least in part, from the embryonic notochord.
The tuatara spine is made up of hourglass-shaped amphicoelous vertebrae, concave both before and behind. This is the usual condition of fish vertebrae and some amphibians, but is unique to tuatara within the amniotes[Wikipedia].
Spool-shaped vertebral centrum with an open center in which the notochord lies.
Spool-shaped vertebral centrum with a solid center. All traces of the notochord dissapear.
Vertebral centrum that is depressed dorsoventrally and solid. All traces of the notochord dissapear.
Paired plates that form the haemal arch. The lateral margin of each lamina is firmly attached to the ventral surface of the caudal vertebral centrum and the medial end fuses to the medial end of the opposite lamina.
Longitudinal process found in all cervical vertebrae, except the atlas, for the attachment of dorsal head musculature.
Opening on the lateral side of the vertebra for the passage of blood vessels.
Ridge-shaped structure present on the dorsomedial surface of the neural arch lamina; this structure is produced at the point of junction of the contralateral sides of each neural arch.
Ridge on the ventral aspect of the humeral shaft. It serves for the attachment of the mm pectoralis and shoulder musculature used primarily for limb adduction.
Anterior, paired convex facets for articulation with the cotyle(s) of the urostyle.
Anterior, single or paired concave facets for articulation with the sacral condyle(s).
In anurans, pair of bony plates that connect the posteromedial margins of the sacral diapophyses with the lateral margins of the anterior portion of the urostyle.
Longitudinal crest on the dorsal side of the urostyle formed by the caudal neural arches.
Paired, cartilaginous elements located in the dorsolateral shoulder region. Each suprascapula is a flat broad blade that extends medially.
Prominent structure (anteromedial head) that forms the anterior section of the ventral margin of the scapula.
Concave structure (posteromedial head) that forms the posterior head of the ventral margin of the scapula. The pars glenoidalis articulates with the humerus, and comprises the dorsal portion of the glenoid fossa.
Small hooked process on the dorsal aspect of the humeral shaft; it does not extend on to the glenoid head. The m subscapularis is inserted on it.
All those parts of the pectoral girdle ventral and medial to the glenoid fossa.
Proximal portion of the prezonal element of the pectoral girdle. It may be a flat, midventral cartilaginous structure or a calcified or bony element elaborated into a stylum.
Paired, flat cartilaginous arches that compose the central portion of the zonal area, unites the clavicle and coracoid of each half of the pectoral girdle, and form the medial margins of the pectoral fenestrae.
A pair of cartilaginous expansions (one from each epicoracoid cartilage) that project anteriorly. They articulate anteriorly with the omosternum.
The central, most concave portion of the acetabulum, which remains open.
Longitudinal crest on the dorsal side of the shaft of the ilium.
Anterior rod that articulates with the sacrum.
Posterior body of the ilium that forms the anterior half of the acetabulum.
A pair of cartilaginous expansions (one from each epicoracoid cartilage) that project posteriorly. They articulate with the sternum by means of grooves, pouches or fossae in the dorsal surface of the sternum and provide a site for the insertion of a pair of muscles derived from the m. rectus abdominis.
Opening on the scapulocoracoid bone through which passes the n. supracoracoideus and the corresponding artery and vein.
Ovoid space on the pectoral girdle limited anteriorly by the procoracoid, medially by the epicoracoid, and posteriorly by the coracoid.
fenestra between procoracoid and coracoid
Notch that separates the cartilaginous regions of the procoracoid and coracoid.
Ovoid roughened pit, which is situated a little below and behind the center of the head, and serves as a site of attachment for ligaments.
Not to be confused with the fovea capitis of the femur
Semi-elliptical ball located at the lower end of the humerus, adjacent to the humeral ball.
Furrow between the humeral head and the ulnar condyle.
Depresion on the distal end of the humerus, just anterior to the humeral head, in which the end of the radius fits when the forelimb is flexed.
In a fused radio-ulna, the proximal portion of the compound bone (where the sulcus longitudinalis is barely evident or absent) is a cylindrical pillar.
Subdivision of the cleithrum that extends along the anterior edge of the suprascapula.
Stegochordal slightly biconcave or flat terminally vertebral centrum. Each intervertebral cartilage is subdivided anteriorly and posteriorly, producing a free intervertebral element between adjacent vertebrae. This element subsequently ossifies and remains free.
Vertebral column in which the first seven vertebrae have holochordal centra and the intervertebral cartilages are posteriorly subdivided in the procoelous manner. The eighth presacral vertebra has a holochordal centrum and the intervertebral cartilage is subdivided in the opisthocoelous manner. Thus, the first seven presacral vertebrae are concave anteriorly and convex posteriorly, whereas the eighth is biconcave.
Overlapping neural arches that obscure the spinal cord dorsally.
Neural arches that do not overlap, thus exposing the spinal cord dorsally.
Dorsal, dermal plate of bone that overlies the presacral vertebrae. Such shield usually has irregular, sculptured surfaces, frequently is broadly expanded, and may be composed of several separate plates.
Strip of cartilage that separates the coracoid from the scapula.
Convex articular facet of the vertebral centrum for the articulation with the adjacent centrum.
Concave articular facet of the vertebral centrum for the articulation with the adjacent centrum.
In a zygapophysis that has ridges and sulci, the lateral canal between the carina distalis and the carina medialis.
In a zygapophysis that has ridges and sulci, the medial canal between the carina medialis and the carina proximalis.
In a zygapophysis that has ridges and sulci, the proximal ridge.
In a zygapophysis that has ridges and sulci, the medial ridge.
In a zygapophysis that has ridges and sulci, the distal ridge.
Paired, posteriorly directed process at the posterior margin of each neural arch lamina.
Paired, additional vertebral articulations located medial to the intervertebral space, adjacent to the vertebral centrum.
Medial groove in the longitudinal ridge of the urostyle formed by the incomplete dorsal fusion of the caudal neural arches.
Lateral end of the clavicle, which usually lies in close proximity to the pars acromialis of the scapula, and occassionally may fuse to it.
Canal on the posterior aspect of the clavicle that accomodates the anterior margin of the procoracoid cartilage.
sulcus pro cartilagine praecoracoidealis
Lateral end of the coracoid, which forms the medial portion of the glenoid fossa.
Medial end of the coracoid, which is synchondrotically fused to the epicoracoid cartilage.
Anterior margin of the coracoid, which forms the posterior edge of the pectoral fenestra.
Inferior margin of the pars acromialis of the scapula, which articulates with the clavicule.
Superior margin of the scapula, which articulates with the suprascapula.
Superior portion of the scapula, which is thinner than the rest of the shaft.
Notch or indentation between the pars glenoidalis and pars acromialis of the scapula.
Leading (anterior) portion of the scapula, which is thinner than the rest of the shaft.
Longitudinal ridge on the medial (inner) face of the scapula.
Anterior margin of the anterior ramus of the cleithrum.
Posterior margin of the posterior ramus of the cleithrum.
Lateral margin of the suprascapula, which articulates with the scapula.
Medial margin of the suprascapula, which lies dorsal to the vertebral column.
Small process of the lamina recurvata that extends laterally toward the scapular-suprascapular articulation.
Portion of the anterior ramus of the cleithrum that invest the anterior margin of the suprascapula, extending onto its dorsal surface.
Notch or indentation between the anterior and posterior rami of the cleithrum.
Portion of the posterior ramus of the cleithrum that invests the posterior margin of the suprascapula, extending onto its dorsal surface.
Ridge on the lateral aspect of the humeral shaft located just anterior to the radial (lateral) epicondyle.
Ridge on the medial aspect of the humeral shaft that extends from the level of the middle portion of the shaft to ulnar (medial) epicondyle.
Small ridge on the lateral aspect of the radial shaft, located at the level of the collum antibrachii.
Lateral portion of the proximal (upper) articular surface of the radius that consists of an eminence with a rounded apex.
Small eminence on the distal articular head of the radius.
Small eminence on the distal articular head of the ulna.
In a fused radio-ulna, longitudinal furrow that demarcates the area of fusion of both elements. This sulcus is deep in the distal portion of the compound bone, but barely evident or absent at the proximal end.
Oval carpal element that is located on the anteromedial side of the radiale and the anterolateral side of the ulnare. Anteriorly, it articulates with carpals 1 through 4 (or 2 through 5 according to some authors). It is also recognized as centrale by some authors. This element originates from one, two, or three condensation centers. Occasionally it may fuse to carpal 2(1), carpal 3(2), the ulnare, or other elements.
Small elements present in all digits of the manus, when present in a taxon. Each intercalary element articulates with the anteroventral end of the penultimate phalanx proximally and the distal phalanx distally.
Opening for the passage of the perforans carpi artery from the ventral to the dorsal side. It perforates the compound ulnare + intermedium.
Composite element formed by the fusion of the ischium and pubis.
Dorsal extremity of the ilial shaft, which remains cartilaginous.
Shelf-like expansion of the ilial corpus that forms the anterior border of the acetabulum.
Shelf-like expansion of the ischium that forms the posterior border of the acetabulum.
Dorsal portion of the ilial corpus, located above the acetabulum.
Small, dorsolaterally projecting knob located just anterior to the supra-acetabular expansion and about the level of the anterior border of the acetabulum.
Ventral portion of the ilial corpus, located anteroventral to the acetabulum.
Small depression dorsal to the proximal portion of the collum ilei and ventral to the ilial protuberance.
Cyllindrical pillar that originates anterior to the acetabulum and extends to the ilial shaft.
Elongate, cylindrical structure on the ventral side of the shaft of the ilium that extends through its entire length.
Crest on the posterior side of the ischium, which may also extend to the posteroventral aspect of pubis.
Small, rounded process on the anterodorsal margin of the ischium, just posterior to the area of articulation with the ilium.
Small, rounded process on the anteroventral margin of the preacetabular expansion of the ilial corpus.
Small protuberance on the ischium, located close to its posteroventral margin.
Small protuberance on the ischium, located at the level of the superior margin of the acetabulum and close to its posterior margin.
Small indentation on the posterior margin of the ischium, ventral to the intumescentia bilateralis superior.
Large protuberance on the dorsal aspect of the ischium that extends from the ischio-ilium articulation to the spina pelvis posterior.
Area of convergence of the ilial shafts. When the preacetabular ilium is narrow, the interilial configuration is V-shaped or narrowly rounded, whereas when the interilial region is broadly expanded the interilial configuration is U-shaped.
Area dorsal to the pelvic girdle symphysis, between the dorsal portions of the ilial corpora, where lies the posterior terminus of the urostyle.
Small prepubic element formed by a plate of cartilage (which may calcify in the adult) that is synchondrotically united with the pubis.
Paired cartilaginous rods that lie within the copulatory organ (or so-called tail) and are attached to the posteroventral part of the pelvic girdle.
Y-shaped cartilage lying in the middle line, anterior to the pubo-ischium with which it articulates. It lies dorsal to the rectus abdominis muscle with which it articulates.
Low crest that arises just behind the acetabular head and extends distally for about one-third the length of the femoral shaft.
Canal on the posteroventral surface of the femoral head, which articulates with the ischial process on the rim of the acetabulum.
Ovoid roughened pit situated on the dorsal and anteroventral surface of the acetabular head wherein the ligaments attaching the bone to the acetabulum are inserted.
Paired ridges on the ventral surface of the femoral shaft that run toward the femoral trochanter; the posterior crest is less developed.
Ridge that arises from the dorso-masial side of the extensor surface of the tibia. It receives the insertion of the tendon of the extensor ilio-tibialis muscle.
Swelling on the extensor surface of the distal head of the tibiofibula.
Proximal head of the tibiofibula that articulates with the distal head of the femur.
Small canal on the proximal head of to the tibiofibula, lateral to the apophysis distalis, for the insertion of the cruris brevis muscle.
sulcus pro musculo extensori cruris brevis
Small crest on the extensor surface of the proximal head of the tibiofibula (tibial side).
In a fused tibiofibula, longitudinal furrow in the distal portion of the compound bone that demarcates the area of fusion of both elements.
In a fused tibiofibula, longitudinal furrow in the proximal portion of the compound bone that demarcates the area of fusion of both elements.
Foramen for the tibial artery and vein and the deep peroneal nerve; it pierces through the midpoint of the shaft of the tibiofibula.
Separation of the tibiale and fibulare along their longitudinal axia.
Swelling on the extensor surface of the proximal compound head of the tibiale and fibulare.
Swelling on the extensor surface of the distal compound head of the tibiale and fibulare.
Oval tarsal element that is located on the anteromedial side of the tibiale. Anteriorly, it articulates with the proximal prehallux, tarsals 1, 2, and 3.
One to three or four elements located ventral and medial to the metatarsal of digit I. When more than one elements are present, they are smaller than the proximal prehallux.
This class was sourced from an external ontology (amphibian_anatomy). It was modified by cjm in the following way: the class was relabeled from 'prepollex' to 'prepollex skeleton', to distinguish it from the digit-like structure which it is a part of. It was re-classified from bone to subdivision of skeleton, as it may in fact be composed of multiple individual bones. TODO: definition needs reviewed, and it still requires placement under the UBERON:0012136 ! prehallux
Small elements present in all digits of the pes, when present in a taxon. Each intercalary element articulates with the anteroventral end of the penultimate phalanx proximally and the distal phalanx distally.
Small opening between the centrale and fibulare that allows the perforans tarsi artery to pass from the ventral to the dorsal side of the ankle.
Dorso-lateral portion of the pectoral girdle.
All those parts of the pectoral girdle in the central region of the zonal area.
All those parts of the pectoral girdle that lie anterior to the zonal area.
All those parts of the pectoral girdle that lies posterior to the zonal area.
Pectoral girdle in which the epicoracoid cartilages are elaborated into posteriorly directed epicoracoid horns. Most arciferal pectoral girdles are characterized by fusion of the epicoracoid cartilages in the interclavicle region. Posterior to the clavicles, the epicoracoids usually are free and overlapping.
Pectoral girdle that lacks epicoracoid horns. The sternum is fused to the pectoral arch, and the epicoracoid cartilages of each half of the girdle are fused to one another. The midzonal length of the girdle is shorter than that of an arciferal girdle, but pre- and postzonal elements tend to be longer.
Modified arciferal pectoral girdle in which the fusion of the epicoracoid cartilages in the interclavicle region is extended posteriorly. Thus, the cartilages no longer overlap freely, and functionally a partially firmisternal condition is created.
Modified firmisternal pectoral girdle in which the epicoracoid cartilages are partly free and overlapping; however, the epicoracoids are fused to one another and the sternum postermodially.
Three pairs of cartilaginous elements posterior to the sternum that lie in the myosepta of the ventral trunk musculature.
Paired processes located on the anterior end of the cricoid cartilage.
Laminar subdivision of the cleithrum that extends along the ventral (lateral) midbody of the suprascapula.
Small, broadly triangular bar of bone lying across the ventral side of the pharynx at the junction of the M. genio-hyoideus and the M. rectus cervicis superficialis.
Paired, horn-like processes of basibranchial I that protrude in an antero-dorso-lateral direction, being more or less embedded in the tongue musculature. These elements contitute the hypohyals.
Paired, horn-like processes of basibranchial I that protrude in an antero-dorso-lateral direction, being more or less embedded in the tongue musculature. They arise secondarily during metamorphosis, and are therefore not strictly part of the visceral skeleton.
Paired bars that articulate with hypobranchial II. Reduction of loss of these elements is common in salamanders.
Paired bar that articulates with basibranchial I. It forms the anterior portion of the posterior cornu of the hyoid.
Paired bar that articulates with, or is fused to, hypobranchial I. It forms the posterior portion of the posterior cornu of the hyoid.
Paired bar that articulates anteriorly with basibranchial I and posteriorly with ceratobranchials II--IV.
Paired, anterior element that articulates medially with basibranchial I and posterolaterally with the paired hypohyals.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
Dermal bone of anuran lower jaw investing lingual and ventral surfaces of Meckel's cartilage; forming coronoid process and articulating with palatoquadrate posteriorly.
redundant with stage+skeletal system. Can be properly reinstated if needed.
Dermal, epidermal, glandular and pigment structures of the external head integument.
Dermal, epidermal, glandular and pigment structures of the body integument.
Dermal, epidermal, glandular and pigment structures of the limb integument.
Dermal, epidermal, glandular and pigment structures of the tail integument.
Larval upper jaws articulate with trabecular horns.
obsolete palatoquadrate and suspensorium
Mechanoreceptive organ of the lateral line, smaller than neuromasts, they are located on the surface of the epidermis. These receptors receive afferent and efferent innervation.
Originates from the superior process of the ilium and inserts on the aponeuronis of the M. cruralis.
Originates on the ventro-lateral aspect of the ala ossis ilei and the ventral surface of the iliacus externus. Inserts on the lateral surface of the cruralis, the dorso-lateral surface of the gluteus magnus, and on the aponeurosis of the cruralis.
Originates on the ventral pelvic rim, the pubic region, and the ventral surface of the adductor longus. The insertion bifurcates distally; the ventral portion attaches to the aponeurosis of the cruralis and the dorsal part attaches to the distal attachment of the gracilis major, the semitendinosus, and to the aponeurosis of the cruralis.
Multi-cellular organism that has male and female sexes.
Originates by two tendons: one on the postero-ventral aspect of the pelvic rim, the other, a dorsal tendon from the postero-dorsal pelvic rim under the ventral edge of M. semimembranosus. Inserts on the ventral surface of the tibiofibula.
Sequential hermaphroditic organism that produces gametes first of the male sex, and then later of the female sex.
Sequential hermaphroditic organism that produces gametes first of the female sex, and then later of the male sex.
Distal-most centrale when two are present.
Originates on the ventro-lateral border of the ischium and inserts on the ventro-medial surface of the femur at the base of caput femoris.
Originates from the dorso-lateral margin of the ischium and inserts on the medial surface of the femur.
A dermal fold surrounding the body reflecting body segmentation. Found in Caecilians.
Rectangular cartilage or bone between the distal basal commune and the proximal intermedium.
Cartilage that bridges palatoquadrate to ethmoid region.
Originates by a broad tendon from the postero-ventral surface of the pelvic rim and inserts by two tendons. One broad tendon inserts on the knee aponeurosis, and in part on the ventro-medial surface of the tibiofibula. The other long tendon inserts on the posterior surface of the tibiofibula just below the proximal head.
Originates from the pelvic rim just ventral to the anus and merges with M. gracilis major. M. gracilis minor also attaches to the skin.
Originates on the ventro-lateral surface of the ischium below the anus and inserts on the ventro-medial aspect of the femur and the head of the tibiofibula by a stout tendon, which is formed by the ventral origin of the plantaris longus.
Quadrangular cartilage or bone lying between the preaxial radiale and the postaxial ulnare in the proximal level of the mesopodium.
Originates from the ventral border of the ala ossis ilei just posterior to the origin of M. glutaeus maximus. Insterts in the aponeurosis covering the knee joint.
Originates on the dorso-lateral border of the distal urostyle and inserts on the dorsal surface of the crista femoris. This muscle inserts between the M. ilio-fibularis/M. glutaeus magnus and M. semimembranosus.
The proximal-most rectangular cartilage or bone when two centralelia are present.
Originates from the postero-ventral surface of the ala ossis ilei and from the insertion tendon of M. ileo-fibularis. Inserts along the dorso-medial border of the femur.
Muscle originates on the ventral border of the ala ossis ilei to insert on the dorso-medial surface of the femur.
Originates on the ventral and lateral surfaces of the ala ossis ilei and inserts on the postero-dorsal face of the caput femoris.
Originates along the connective tissue covering the dorsal surface of the lung and inserts on the dorsal surface of the femur. Muscle found only in Pipa.
Originates on the entire medial surface of the shaft of the tibiofibula. Inserts on the tibiale by a long tendon proximo-lateral to the insertion of the medial belly of M. tibialis anticus longus.
Originates on the ventro-lateral surface of the medial condyle of the femur. Its tendon extends in a groove over the knee in the lateral surface of the tibiofibular head, and penetrates the M. peroneus tendon. Insertion is by a lateral and medial head on the dorso-lateral surface of the fibulare and the medial border of the proximal end of the tibiale respectively.
Originates by a slender tendon from the ventral surface of the medial condyle of the femur and passes over the knee to insert as a fleshy belly on the ventro-lateral surface of the tibiofibula.
Originates from the dorso-lateral surface of the tibiofibula and inserts on the proximo-medial surface of the tibiale dorsal to the medial head of M. tibialis anticus longus.
A process of the otic capsule that will bridge to the palatoquadrate basal process.
Small hair or nipple like projection on the integument.
Process that projects from anterior margin of commissure as site of attachment for quadratoethmoid ligament.
Originates on the medial border of the ligamentum calcanei and inserts along the ventral surface of the tibiale.
Originates on the medial half of the ligamentum calcanei and inserts along the dorsal surface of the aponeurosis plantaris and extends to the level of the base of the prehallux.
Cranial nerve III innervated; dorsal in the rectus group.
Cranial nerve III innervated; ventral in the rectus group.
Sensory nerve of the anterior lateral line component. It develops from the preotic anterodorsal placode. ADLLN branches into two rami innervating orbital lines of neuromasts.
Sensory nerve of the anterior lateral line component. It develops from preotic anteroventral placode. AVLLN innervates lower jaw lines of neuromasts.
anteroventral lateral line nerve (AVLLN)
Cranial nerve III innervated; medial in the rectus group.
Sensory nerve of the posterior lateral line component. It develops from de postotic posterior placode. PLLN innervates the trunk lines of neuromasts.
Cranial nerve III innverated; ventral in the obliquus group.
Cartilage that bridges palatoquadrate muscular process to dorsal orbitonasal plate.
Cranial nerve V innervated; ventral to the eye.
Sensory nerve of the posterior lateral line component. It develops from the postotic middle placode. MLLN innervates neuromasts located over the otic capsule and the suprabranchial line of neuromasts.
Kok & Castroviejo-Fisher (2008) Zootaxa.
Compose lateral rim of frontoparietal fenestra, ventrally confluent with orbital cartilages, posteriorly confluent with tectum synoticum.
Cartilaginous connection that partitions frontoparietal fenestra into anterior and posterior regions. Often persists form larva into adults.
Forms lateral walls of braincase, confluent posteriorly with otic capsules via taenia tecti marginalis and anteriorly with lamina orbitonasalis via sphenethmoid commissure.
Cartilaginous connection between the taenia tecti transversalis to the tectum synoticum, and subdividing the parietal fenestra into left and right fenestrae. Often persist from larva to adult.
Originates from the anterior surface of the hip joint capsule between the iliacus internus and the pectineus. Inserts by an aponeurosis attaching to the condyles of the femur and on the head of the cruris. This continues over the cruris to cover the tibialis anticus longus and peroneus to insert on the dorsal surface of those muscles.
Ventral plate anterior to and confluent with ethmoid plate.
Posterior chondrocranium forming ventral and lateral margins of foramen magnum, medial to otic capsules.
Toothlike processes found on the mandible of some anurans; can be formed by dentary or dentary + mentomeckelian bones; odontoids lack enamel and dentine present in true teeth.
Plate of cartilage occluding fenestra ovalis.
Investing bone associated with nasolacrimal duct and lying between pars facialis of maxilla and prefrontal and sometimes nasal.
replaced with 'olfactory epithelium support cell' due to axiom (removed) that it was part of olfactory epithelium.
Obsoleted as it had no definition or logical axiom beyond being placed as an 'olfactory 'epithelium', which is incorrect for a cell (should be part of). If a definition is found we can rescuscitate this class.[UBERON:cjm]
Is a integumentary structure located on the ventral surface of the hand and/or foot. Found at the junction between, in the hand, the metacarpal and most proximal phalanx of the digit and between phalanges, and in the foot between the metatarsal and most proximal phalanx of the digit and between phalanges.
A recurrent variant of salamanders; a rhomboidal cartilage lying immediately postaxial from the centrale or centrale 1.
A small lateral diverticulum of the nasal cavity found in anuran larvae.
A part of the inferior cavity of the olfactory organ, found in anurans.
A rounded cartilage lying in the postaxial margin of the mesopodium, adjacent to the distal end of the fibulare.
Often consider atavistic when present in extant salamnders (Caudata)
Either of two arteries which carry blood to the head.
An artery which supplies blood to the muscles of the tongue and floor of the mouth via four major branches.
An artery which supplies the upper jaw and cranium.
An anatomical cluster that is part of the cranium and structurally supports the eye.
Either of a pair of cartilaginous rods that support the intromittent organ of male Ascaphus, and are attached to the posteroventral part of the pelvic girdle.
Eversible phalloid portion of the cloaca that is inserted in the female's vent during copulation. Found in male Caecillians.
A tail like posterior extension of the cloaca supported by a pair of Nobelian rods
Multi-cellular organism that does not produce gametes.
Anatomical space that is part of a cell.
Cell which has as its part a cytoskeleton that allows for tight cell to cell contact and which has apical-basal cell polarity.
Cell that is an individual member of a species.
Pigmented, smaller blastomere of the animal (upper) hemisphere of the cleaving embryo.
Unpigmented, larger blastomere of the vegetal (lower) hemisphere of the cleaving embryo.
Cell type that is first to migrate inwards at the blastopore during gastrulation.
replace with CL:0000020 once cl is released.
Polymorphic cell type that forms cartilage.
A connective tissue cell that secretes an extracellular matrix rich in collagen and other macromolecules.
Primitive cell type that is involved in the reproduction of the organism beginning with the sexual differentiation of the gonads at NF stage 52. In males specifically, it migrates from the genital ridge cortical region into the medullary tissue, where it forms spermatogonia. In females it is embedded in the cortical region and multiplies as oogonia.
A mature male germ cell that develops from a spermatid.
A germ cell that is a primordial oocyte in a female and that develops into secondary oogonia by mitotic division.
A germ cell that is a primordial spermatocyte in a male and that develops into secondary spermatogonia by mitotic division.
A type of germ cell that results from the mitotic division of a primary oogonium.
A type of germ cell that results from the mitotic division of a primary spermatogonium.
A large distinctive organelle aggregate comprised of mitochondria found in developing oocytes of many species. From Pepling et al. 2007.
A cell of the B cell, T cell, or natural killer cell lineage.
A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive.
A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
An immature T cell located in the thymus.
Embryonic (precursor) cell of the myogenic lineage that develops from the mesoderm.
The myoblast that forms the muscles of the anterior abdominal walls.
Cell that is the basic unit of nervous tissue, each consisting of a body, an axon, and dendrites, and the purpose of which is to receive, conduct, and transmit impulses in the nervous system.
Cell type that contains a deposition of coloring matter.
A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platets or iridisomes. The color-generating components produce a silver, gold, or iridescent color.
A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red.
Cell type that is a component of the glomus.
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system.
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
The first appearance of the antomical space that will become the blastocoel.
replaced with pigment epithelium of eye because was previously asserted to be part of a camera-type eye.
Skeletal and cartilaginous elements of the branchial arches; the last five of the set of seven pharyngeal arches; the numbering system can be confusing; generally branchial arch #1 is the first branchial arch, or the third pharyngeal arch, but some authors do not follow this convention.
Part of the fin consisting of a supporting core of mesenchyme and extracellular matrix.
Part of the fin consisting of flattened epidermal cells elevated into a keel-like structure.
In frogs (Anura) the outer fin tissue is present only in tadpoles and sometimes during the embryogenesis of species without tadpoles. In salamanders and caecilians tail fins can persist into reproductive maturity.
The site of bicarbonate resorption in the adult kidney. It is equivalent to the convoluted distal segment of metanephric nephrons. [Xenbase]
The smallest of the blood vessels, parts of the microcirculation, of the liver.
It arises on the lateral epicondyle of the humerus by two heads: the lateral one arises by a thin tendon in common with the m.extensor carpi ulnaris with fibers proximally fused. The internal one arises by a short tendon in common with proximally fused fibers of the m. extensor carpi radialis. It divides distally in two heads: the external head inserts with a long and thin tendon on the metacarpal V, at the same point of insertion of the m. abductor brevis dorsalis digiti V; the internal one inserts by a thin tendon on the proximal region of the metacarpal IV, between the m. extensor brevis superficialis digiti IV and the m. extensor brevis medius digiti IV (Pristimantis bogotensis).
Marginal zone that is a key embryonic tissue region of the early gastrula stage embryo and that houses the Spemann-Mangold organizer.
Part of the external carotid which delivers blood to the mm rectus cervicis and interhyoideus posterior.
Part of the internal carotid which supplies blood to the ear and branches to two additional arteries.
Part of lateral pretrosal artery which supplies blood to the roof of the mouth.
Artery which supplies blood to the thymus and parotoid region.
This artery has many branches which supply blood to various organs in the viscus.
Major branch which supplies blood to the spleen and dorsal wall of the stomach.
Major branch which supplies blood to pancreas and duodenum.
Major branch supplying blood via many smaller branches to the liver, duodenum, ventral wall of the stomach, and gall bladder.
One of three arteries which are part of the renal artery supplying blood to the anterior, middle, and posterior parts of the oviduct.
One of three major veins which enter the sinus venosus.
Either of a pair of veins which enter on either side of the sinus venosus.
Either of the veins which collect blood from the trunk and skin and drain into the subclavian vein.
A vein formed by the combination of veins in the pelvic region which collects blood from the liver, stomach, intestines, and gall bladder.
Either of a pair of veins which receives many small vesicles from the kidney and collects blood from the oviducal vein.
Vein which collects blood from the oviduct.
Originates by two heads, one from the dorso-distal border of the aponeurosis covering the knee and the other from two tendinous branches along the medial border of the knee joint. Inserts by a thick, broad tendon to form the aponeurosis plantaris.
Either of the short tubes which bifurcate posteriorly from the trachea and lead into the lungs.
Part of the ovary consisting of a thin sheath of connective tissue enclosing the ovarian follicles.
A thin membrane which attaches the testes to the kidneys and supports the efferent ductules from the testes to the kidneys.
Region of the neurohypophysis which secretes neurohypophyseal hormones, regulating water loss and salt balance.
Region of the adenohypophysis which secretes melanophore-stimulating hormone, affecting the integumentary chromatophores.
A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers.
An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).
A cell of the outer of the three germ layers of the embryo.
A cell of the inner of the three germ layers of the embryo.
A cell of the middle germ layer of the embryo.
retroarticular process of the palatoquadrate
A strut of cartilage extending dorsally from the basal plate and with other similar cartilages forming the sides of the brain case. Posterior to the pila preoptica is the pila antoptica between these two cartilages emerges the optic and trochlear nerves.
A dermal bone that forms anterior to the premaxillae between the maxillae and articulates with the nasals posteriorly.
Bilaterally unpaired ventral element with which articulates with lateral paired elements.
Anterior most migratory stream of cranial neural crest.
Unpaired medial element that articulates with the anterior basibrachial I (if present).
Sperm travel through these 4 or 5 fine ducts which pass through the mesorchium from the testis to the sexual kidney.
Population of cranial neural crest that give rise to hyoid arch elements.
A small, ridge-like projection from the antero-ventral wall of the cloacal chamber.
A structure that surrounds the cloacal opening, consisting of a mass of coarse tubules.
Note that this class originally had axiom that it was part of the integument. However, the term had no definition and one can use the general erythrophore def from CL.
A gland that contains toxic secretions within the lumen. In frogs and salamanders, this is the larger of the two types of gland, the other being the mucuous gland[Kardong]
Muscular vestibule between the pharynx and lungs, lying between the posterior cornua of the hyoid.
A series of semicircular cartilages on the side of the laryngo-tracheal chamber.
cartilago lateralis of aryngo-tracheal chamber
Involved in the movement of the arytenoid cartilages.
Is an endochondral structure located on the ventral to the junction between, in the hand, the metacarpal and most proximal phalanx of the digit and between phalanges, and in the foot between the metatarsal and most proximal phalanx of the digit and between phalanges. Typically subarticular sesamoids are found with the subarticular tubercles.
A transient rod-like structure ventral to the notochord in salamander embryos. Derived from endoderm.
A type of mucus and/or fluid secreting cell in larvae.
Innervates m. rectus superior (m. dorsal rectus).
obsolete dorsal ramus of occulomotor nerve
Possibly chemoreceptor cells in anuran larvae.
replace with CL_0007017 once CL is released.
Innervates m. rectus medialis, m. rectus inferior, m. obliquus inferior.
obsolete ventral ramus of occulomotor nerve
Type of cell that appears in epidermis during metamorphosis and is rich in mitochondria.
replaced by CL_0007023 once cl is released.
A mucous surface cell type known in tadpoles of Xenopus.
Protective membranes that surround amphibian embryos.
Type of mucous-producing cell that appears in early larval stages and persists after metamorphosis.
replace with CL_0007019 once cl is released.
A type of cell that develops in embryos and functions in embryonic movements.
replace with CL_0007018 once cl is released.
One of the principal muscles used in swallowing.
First branch gives rise to two ramules that border the naris and innervate the surrounding tissue.
Retracts the hyoid and, therefore, the tongue.
Deep, visceral muscle associated with tongue movement.
Distal part of the opthalmicus profundus gives rise to 2 ramules: palatinus and cutaneous.
Ramules that descends towards the buccal roof and give rise to several short branches that anastomose with palatine ramus of the facial nerve.
Many branches of the maxillary ramus that terminate in the integument of the maxillary region.
Portion of the trigeminal nerve where the maxillary and mandibular rami run together prior to bifurcating.
Descends and branches to the buccal roof where it anastomoses with the palatine ramus of the facial nerve.
Muscle which originates on the posterior surface of the frontoparietal and the anterior part of the dorsal fascia. Inserts on the ventral surface of the anteromedial corner of the suprascapula.
Endochondral element distal to terminal phalanx of hind digit.
bony nodule of terminal phalanx of hind digit
Is the proximal-most prepollical element.
Type of deciduous dentition found in foetuses and altricial juveniles of some caecilians.
Muscle which arises from the dorsal m. levator scapulae and extends between the operculum and suprascapula.
Muscle which originates on the prootic and the otic ramus of the squamosal and inserts on the anterior border of the suprascapula.
In the adult anuran, this innervates the muscles levator mandibulare internus and longus.
Muscle which originates from the transverse process of presacral vertebrae IV and insert on the dorso-medial surface of the suprascapula.
Muscle which originates from the transverse process of presacral vertebrae IV and inserts on the dorso-medial surface of the suprascapula beneath the insertion M. rhomboideus posterior.
Muscle which originates from the transverse process of presacral vertebrae III and inserts on the central and medial surface of the suprascapula.
Muscle which originates as a posterior and anterior head. The posterior head originates from the transverse process and cartilaginous epiphysis of presacral vertebra IV. The anterior head originates on the same parts of presacral vertebrae III. Both insert on the medial surface of the suprascapula near its postero-ventral edge.
Muscle which originates from the ventral surface of the dorsal fascia and inserts on the deltoid crest of the humerus.
Muscle which originates on the lateral surface of the suprascapulae and inserts on the deltoid crest of the humerus.
Muscle which is responsible for the closing of the jaw.
m. adductor mandibulae anterior articularis
m. adductor mandibulae posterior articularis
Muscle which originates from the ventro-medial surface of the suprascapula and inserts on the ventral surface of the scapula.
levator mandibulae externus superficialis
Muscle which originates on the anterior border of the distal part of the sternal horn and inserts antero-medially on the postero-dorsal surface of the epicoracoid cartilage.
The posttrematic branch of the facial nerve, both motor and sensory in function.
Sensory branch of facial nerve from palatal region.
Muscle which originates from the omosternum and epicoracoid cartilage and inserts on the proximal radioulna.
Branchiomotor branch of the glossopharyngeus nerve innervating the m. subarcuales rectus I.
ramus muscularis of glossopharyngeus nerve
Round, flat bone or cartilage that lies in the fenestra ovalis and articulates with the columella.
Muscle which originates as a long belly from the dorsal coracoid near the sternum and inserts on the shaft of the humerus.
Muscle which originates on the dorsal surface of the coracoid and scapula and inserts on the deltoid crest of the humerus.
Muscle which originates from the medial condyle of the humerus and inserts on the carpus.
Formed by fibers from the anterior semicircular canal and sacculus.
Composed of two rami: a short ventral ramus innervating the cochlea (lagena and papille basilar), and a long dorsal ramus innervating the posterior semicircular canal.
Originates from the medial epicondyle of the humerus and inserts on the palmar aponeurosis.
Originates on the ulnar aspect of the radioulna and inserts on the palmar aponeurosis.
Originates on the medial epicondyle of the humerus and inserts on the radial aspect of the radioulna.
Originates along distal third of the ulna and inserts on the ulnare.
Originates as a superior and inferior head. The superior head originates on the outer edge of the humerus and the inferior head originates on the lateral epicondyle of the humerus. Both bellies converge to form a tendon, which inserts on the carpus and the extensor tendon of digit I.
M. flexor antibrachii lateralis superficialis
Originates on the lateral epicondyle of the humerus and inserts on the lower ridge of the radioulna.
M. flexor antibrachii lateralis profundus
Originates on the lateral surface of the urostyle and inserts on the neural arch of the sacrum or on the sacral diapophysis.
Originates on the lateral surface of the urostyle and passes ventral to the sacral diapophysis to insert on the anterior and medial surfaces of the ilial shaft.
Originates on the anterior and lateral aspect of the ilial shaft and inserts on the transverse processes of presacral vertebrae IV-VII.
Major branch of the vagus supplying parasympathetic innervation to viscera.
Motor nervous branch of the vagus innervating m. subarcualis rectus I.
Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx.
Dorsal branch of ADLLN that innervates supraorbital line of neuromasts.
Originates from the posterior tip of the urostyle and inserts on the cloacal musculature and the overlying skin.
Ventral ramus of the ADLLN that innervates the infraorbital line of neuromasts.
A branch of the vagus nerve innervating heart, stomach, and lung muscle.
Runs together with motor fibers of the hyomandibular trunk of VII. The mandibularis externus of AVLLN branches into three ramules .
Originates on the postero-dorsal edge of the postzygopophyses and insert on the dorsal surface of the neural arch of the posterior, adjacent vertebra.
This ramule innervates the jugal line of neuromasts and is the dorsal branch of the ramus mandibularis externus.
Originates on the posterior margin of the suprascapula and the epaxial fascia and inserts ventrally on the lateral fascia of the M. rectus abdominus and the ilial shaft.
A muscular sheet in which the fibers run in right angles to those of the m. oblique externus, slanting downward anteriorly. This is one of three sheets composing the flank musculature.
A component of the rectus abdominal muscle that is some taxa.
A component of the rectus abdominal muscle that is some taxa (see comment) forms a disctinct and separate muscle.
In salamanders (Caudata) the m. rectus abdominis profundus is sometimes continuous with the m. rectus cervicis profundus. In extreme cases (family Plethodontidae) represents an undivided muscle that arises from the psoterior border of the ischium that proceds uninterrupted to the tongue pad.
Hypaxial muscle in which contraction elevates the ypsiloid cartilage; originates from the anterior edge of the lateral process of the ypsiloid cartilage and insert on the anteriorly adjacent inscription.
Medial branch of the ramus mandibularis externus. This ramule innervates the oral and angular lines of neuromasts.
Ventral branch of the ramus mandibularis externus. This ramule have a superior and an inferior division, both innervating the preopercular line of neuromasts.
Small ramus of the MLLN that innervates neuromasts located at the posterior margin of the otic capsule.
Contraction depresses the ypsiloid cartilage; arises from the anterodorsal edge of the pubis deep to the m. rectus abdominis profundus and spreads anteriorly in a fan shape to insert on the lateral edges of the shaft and the posterior edges of the lateral processes of the ypsiloid cartilage .
Ramulus that innervates the suprabranchial line of neuromasts.
Ramulus innervating the suprabranchial line of neuromasts.
Ventral division of the trunk of the PLLN, this prominent ramus extends over the lateral trunk and caudal musculature innervating the lateral line of neuromasts.
This ramus leaves the postotic ganglionic complex together with the third branchial ramus of X. This ramule innervates the ventral line of neuromasts.
Originates on the internal border of the distal carpal 5-4-3 and inserts on the distal end of phalynx I.
m. flexor indicis superficialis proprius
Peritoneum that surrounds the stomach and intestines.
A projection on the suboccular arch, ventral to the muscular process, that serves as the articulation point for the lateral process of the ceratohyal of the hyobranchial skeleton.
processus triangularis of palatoquadrate cartilage
commissura terminales of hyoid apparatus
Fusion of the occipital segment or occipital ring and otic capsule (Francis, 1934).
Metameric segment forming the back of the skull.
A muscle slip arising from the ventral surface of the mandible by means of the ligament near the site of mandibular articulation. The fibers pass anteromedially and attach upon the ventral surfaces of the principal element of the m. intermandibularis (Tyler, 1971).
A muscle slip arising from the lingual surface of the mandible on each side of the m. submentalis. The fibers pass posteromedially and attach upon the median raphe of the principal element (Tyler, 1971).
A muscle slip arising from the lingual surface of the mandible on the anterior portion of the bone. The fibers pass anteriorly, parallel to the mandible, and attach upon the ventral surface of the m. submentalis (Tyler, 1971).
Portion of organism substance located within a cell.
The formation of bone or of a bony substanc, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Chondrogenic element that is composed of cartilage that is not replaced.
Endochondral bone that is median and is the anterior-most bone of the ventral hyoid arch.
Cell of the notochord, often vacuolated or resembles a chondrocyte.
Cell that has the potential to form a skeletal cell type (e.g., cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized).
Epithelial cell that is large, vacuolated, and part of the notochord.
Extracellular matrix that is mineralized.
A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684].
Combination of protein fibers, ground substance and tissue fluid; typically has embedded cells.
Odontogenic papilla that is located in the integument.
Odontogenic papilla located along the jaws or pharyngeal skeleton.
Skeletogenic cell that has the potential to develop into an ameloblast.
Skeletogenic cell that is derived from the notochordal mesoderm and produces notochordal tissue (and cartilage tissue in some taxa).
Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a neural crest cell.
Skeletogenic cell that has the potential to develop into a cementoblast.
Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells.
Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells.
Multi-layer ganoid scale composed of ganoine and cellular bone.
Thick, rhomboid-shaped integumentary skeletal element composed of multiple tissues including ganoine and bone.
Connective tissue that is matrix-poor with large number of vacuolated cells.
Multi-tissue structure composed of ganoine, dentine, elasmodine and cellular bone.
Proteinaceous extracellular matrix that is avascular and consists primarily of glycosaminoglycans.
Multi-tissue integumentary element composed dentine, elasmodine, and hypermineralized tissue.
Multi-tissue structure composed of ganoine, dentine and bone; not known in extant taxa.
Skeletal tissue that is mineralized, has large chondrocyte-like cells, sparse extracellular matrix, and minimal perichondrium; develops from non-mineralized chondroid tissue.
Fold or elevation of the epidermis rich in keratin proteins; possibly calcified but does not contain skeletal elements.
Multi-tissue integumentary element composed of enamel or enameloid, dentine and lamellar bone, and characterized by pore-canal system.
Cartilage tissue that is part of the exoskeleton, deposited adjacent to bone after bone formation.
Skeletal subdivision that is part of the extra-oral dermal skeletal system that develops and remains invested within the integument, primarily the dermis.
Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell.
obsolete non-terminally differentiated odontoblast
Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine.
obsolete terminally differentiated odontoblast
Odontoid tissue that typically contains tubules and is acellular.
Odontogenic tissue that is hypermineralized acellular, noncollagenous, covered by an epidermis and often deposited in multiple layers.
Hypermineralized tissue lacking collagen (except Sharpey's fibres), developing in close proximity to the basal cells of the overlying epithelium.
Not clear if this layer is acellular, making a tissue type for now.
Dentine tissue that lacks dentine tubules and that is penetrated by blood capillaries.
Odontogenic tissue that consists of multiple layers of collagen fibers organized in orthogonal or twisted arrangements.
Hyaline cartilage tissue that is not mineralized.
non-mineralized hyaline cartilage tissue
Hyaline cartilage tissue that is mineralized.
Bone tissue mineralized with hydroxyapatite.
Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix.
obsolete terminally differentiated osteoblast
Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone.
obsolete non-terminally differentiated osteoblast
Mineralized bone tissue that always includes non-terminally differentiated osteoblasts and osteocytes.
Avascular GAG-rich matrix that is not mineralized.
non-mineralized avascular GAG-rich matrix
Avascular GAG-rich matrix that is mineralized.
Mineralized bone tissue that has terminally differentiated osteoblasts but lacks osteocytes.
Skeletal tissue that is avascular tubular mineralized matrix, primarily made of dentine that is deposited by odontoblasts that are excluded from the matrix; develops from pre-dentine tissue.
Sesamoid that develops within a tendon, distal to an articulation or joint.
Ossification that does not require the replacement of pre-existing tissues, most often a cartilaginous model.
Replacement element that forms as a replacement of a ligament.
Ossification that requires the replacement of a pre-existing tissue prior to bone tissue formation.
Direct ossification that occurs within mesenchyme with the formation of an osteogenic condensation not associated with a perichondrium.
Direct ossification in which transformation of the pre-existing tissue occurs without dedifferentiation of cells or reinitiation of cell division; direct transformation of a non-bone tissue into a bone tissue.
Replacement ossification wherein bone tissue replaces cartilage.
Intramembranous ossification on the surface of a cartilage element as the perichondrium becomes a periosteum, without replacement of cartilage.
Chondrogenic element that is composed of cartilage during development and has the potential to become replaced by another tissue.
Sesamoid that develops within a ligament, distal to an articulation or joint.
Dermal bone of pectoral girdle that is dorsal to and articulates with the cleithrum.
In sarcopterygians; analogous in position to postcleithrum in actinopterygians.
The caudal fin is the most posterior median fin. It is composed of a complex of modified centra and modified neural and hemal arches and spines.
Skeletal subdivision of dermal bones that may include the anterolateral plate (AL), the spinal process (Sp), and anteroventral plate (AV) and other dermal bones that are part of the pectoral girdle.
A scapular complex is described in placoderms (Goujet and Young, 1995).
Need to review develops_from relationship to actinotrichia. Lepidotrichia require actinotrichia for development, but develops_from may not be appropriate relationship. See Zhang et al 2010 for details. doi:10.1038/nature09137
Lepidotrichium that is part of the pelvic fin skeleton.
Lepidotrichium that is part of the caudal fin skeleton.
Lepidotrichium that is part of the pectoral fin skeleton.
Lepidotrichium that is part of the anal fin skeleton.
Lepidotrichium that is part of the dorsal fin skeleton.
Paired fin that is a bilaterally paired anterior outgrowth located high on the side of the animal, not far behind the orbit, with the posterior extremity corresponding with the expected posterior end of the branchial region.
Suprabranchial fins are anterior outgrowths from the cephalothorax of thelodonts. Typically scale covered. They do not appear to contain skeletal tissues or elements.
Anatomical projection that is composed of bone or cartilage tissue.
Anatomical cluster that is an osteological unit consisting of the astragalus and calcaneum.
TO DO: add astragalus after it has been added.
Flange on the dorsal part of the humerus, associated with extensor musculature of the forelimb (manus. carpus).
Anatomical surface that is part of a skeletal element and articulates with another skeletal element. [NI]
Bony projection (peduncle) that is located on the posterior portion of the ilium, posterior to the acetabulum.
Second most proximal phalanx in manual or pedal digits.
Consider merging with 'intermediate phalanx'
Posterior projection of the interclavicle that extends betwen and sometimes beyond the clavicles. [AD]
Facet of scapulocoracoid with which the pectoral fin radial(s) articulates. Facet of scapulocoracoid with which the pectoral fin radial(s) articulates. Based on Goujet and Young (1995). [PHENOSCAPE: pm]
Distinct notch ventral to the glenoid. [NI]
A bony process at the distal margin of the acetabulum formed by the ischium and/or the ischial peduncle of the ilium. [AD]
Region of the ilium posterior and dorsal to the acetabulum. [AD]
The posterior of the two coracoid elements found in basal tetrapods. Corresponds directly to the 'coracoid' of synapsids. [AD]
Dorsal fin located posterior to the anterior dorsal fin. [WD]
Posterior most of the two 'double heads' of the blade of the ilium in some take. Distinct and separate for the dorsal iliac process. [AD]
A posteriorly directed bony projection from the ilium that is the attachment site of the iliofibularis muscle (see Sumida, 1997). [AD]
Lateral expansion of the parasphenoid. [PHENOSCAPE:BC]
parasphenoid flange
Soft tissue sheath covering the hemipenis.
Facet to accommodate the radius on the distal end of the humerus. [PHENOSCAPE:NI]
radial facet
Hinge in the skull skeleton to allow for kinetic movement of different parts. [PHENOSCAPE:NI]
dermal intracranial joint
Anatomical projection in the distal region of the femur. [PHENOSCAPE:NI]
Soft tissue notch/opening lying on a spiracle.[PHENOSCAPE:NI]
spiracular notch
Anatomical projection in the posterior/distal region of the femur. [PHENOSCAPE:NI]
Rib located anterior to the sacral region. [PHENOSCAPE:NI]
presacral rib
Rib located in the trunk (ribcage) area (i.e. excluding cervical and caudal axial series. [PHENOSCAPE:NI]
trunk rib
Extratemporal bone: Skull bone in the posterior half of the cranium, bordering the squamosal and opercular. [PHENOSCAPE:NI]
extratemporal bone
Anteriorly projecting processes allowing de facto contact between consecutive vertebrae (some soft tissues are also present) via articular facets. [PHENOSCAPE:NI]
prezygapophyses
The medial surface of the iliac blade. Origin site of the iliofemoralis internus muscle and its homologues.
The region of the pubis posterior to the acetabulum.
In some non-avian reptile this terminology refers to a distinct rear facing process of the pubis. In avians and some closely related theropod taxa this term is used to denote the pubis itself which has been rotated to face backwards.
Broad, convex expansion of the coracoid bone below the level of the glenoid. Based on Romer 1956
A type of pectoral fin in which the endoskeletal elements have a main axis that runs through the center of the fin. This creates a bilaterally symmetrical fin. (Modified from Kardong 2012).
Depression on the ventreal side of the femoral head. Associated with the pubioischiofemoralis externus muscle.
Medial facing projection or surface on the anterior ( cranial) region of the cleithrum that is often textured or denticled. This process has two primary functions: 1) its shape enhances the vertical strength of the cleithrum and 2) it forms the edge of the gill chamber and helps to direct water after it has passed over the gills (modified from Clack 2012).
An anatomical projection ventral to the glenoid fossa on the scapulocoracoid that abuts on the cliethrum (if present).
The transverse pelvic ridge is a short crest directly anterior to, and not extending posterior to, the prominent supra-acetabular buttress from Pawley and Warren 2006.
Joint that articulates left and right clavicles.
Caudal fin lepidotrichium located ventral to the notochord.
A distinct bony ridge on ventralsurface of the humeral shaft that corresponds to the attachment site of the pectoralis muscle.
Flange present of the distal region of the humerus, associated with extensor musculature of forelimb.
Surface of a long bone that possess the flexor muscle attachment sites.
Projection on the lateral side of proximal part of the ulna[PHENOSCAPE:ni].
In most tetrapods this corresponds to digits II-IV, but the exact identiy of digits in this region varies taxonomically based on digit numbering.
An anatomical projection venteral to the glenoid fossa on the scapulocoracoid that abuts on the cliethrum.
An enlargement of the distal region of the calcaneum that corresponds to the attachment site for the foot extensor muscles.
Process on ilium located anteriorly to acetabulum.
Fossa on the medial surface on the scapula above the glenoid.
Osteological unit consisting of the astragalus and calcaneum.
Narrow bone that lies ventral to the level of insertion fo the pectoral fin and is sutured to the posterior edges of both the clavicle and cleithrum. Based on Forey 1998.
The presence of this bone is a synapomorphy of coelacanth fishes.
A dorsal fin located anterior to posterior dorsal fin. [WD]
Fossa located on the medial surface of the scapula above the glenoid
Flattened process of the dorsl surface of the astragalus which contacts the tibia anteriorly. [NI]
Foramen that perforates supraglenoid buttress.
A bony projection dorsal to the glenoid articulation on the scapulocoracoid.
In basal tetrapodomorphs this structure braces the scapula on the cleithrum, but this function is lost in derived tetrapods.
A prominent ridge in basal tetrapods on the ventral side of the femur that includes the fourth trochater, internal trochanter and the adductor crest (based on Coates, 1996). [AD]
A bony crest on venteral side of femur that is the attachment site for the adductor muscles. [AD]
Raised surface at the posterior portion of the acetabulum (see Nesbitt, 2011). [NI]
Muscle that is associated with tail flexion. Orginates on one of the first post sacral vertebrae posteriorly and inserts on the posterior edge of the m.puboischiotibialis. (modified from Duellman and Trueb 1994)
Expanded and flattened ventral region of clavicle bone.
Expanded dorsal region of the cleithrum.
Longitudnal bony ridge on tibia, attachment site of the major extensor muscle of the hind limb.
A boney projection on the internal diaphysis of the femur anterior or medial to the intertrochanteric fossa, below the femoral head. Muscle attachment site for ventral muscle mass notably the puboischiofemoralis externus. Modified from Romer 1956
A bony process that corresponds to the attachment site for the forelimb supinator muscles in tetrapods, distal to the deltopectoral crest and anterior to the radial condyle.
A marked depression on the medial side of the scapula blade, often opposite the glenoid region.
A bony protuberance dorsal to the acetabulum on the ilium, confluent with the supraacetabular crest (when present). Acts as a bone brace to prevent excessive femoral abduction and the origin site for part of the M. iliofemoralis.
Anatomical process located in the proximal region of the coracoid in avian theropods, that is hook-shaped. [NI]
The palmar aponeurosis is a fibrotendinous complex that functions as the tendinous extension of the palmaris longus, when present, and as a strong stabilizing structure for the palmar skin of the hand. It has five longitudinal slips that project into the base of each digit and a deeper transverse portion that crosses the palm at the proximal end of the metacarpals bones (from Wikipedia).
Anatomical projection on the ilium, anchoring caudal muscles.
Contact surface between the calcaneum and the astragalus located on the astragalus.
articular surface for the calcaneum on the astragalus
Contact surface between the calcaneum and the astragalus located on the calcaneum.
articular surface for the astragalus on the calcaneum
The astragalo-calcaneal canal forms a foramen between the articulated astragalus and calcaneum when the canal is ossified (Nesbitt, 2011).
Morphological struture denoting the exent of an attachment site for a soft tissue on a skeletal element.
Anatomical projection that is an expansion on the proximal region of the humerus.
Origin of the aponeursis of humeral head of the M. biceps brachii. From Bamuel et al. 1993
A sesamoid found in the found in the ligamentum calcanei of a wide variety of frogs. (based on Nussbaum, R. A. 1982
A cup shaped articular surface on a bone.
A notch or opening in the ventral part of the acetabular rim.
Tuberosity on the posterior surface of the lateral femoral condyle
An internally and externally symmetrical tail (caudal) fin
In Dipnoi, may be secondarily acquired from the homocercal condition by loss of the real caudal fin and the gaining of a new one from dorsal and anal elements, e.g. in Gadidae. http://www.briancoad.com/Complete%20Dictionary%20latest%20version.htm
Type of tail (caudal) fin in which the vertebral column turns upwards into the upper lobe which is longer than the lower. Asymmetrical externally as well as internally.
Elasmobranchii, Acipenseridae, Polyodontidae and in many larval Teleostomi. May also be used for an asymmetrical caudal fin but with epicercal defining upper lobe longer and hypocercal the lower lobe longer. http://www.briancoad.com/dictionary/DicPics/heterorercal.htm
Type of tail fin in which the vertebrae generally turn upward at the hind end of the column, but which is externally symmetrical. The fin rays of the caudal are supported by hypaxial elements
Found in most Teleostei. http://www.briancoad.com/dictionary/DicPics/homocercal2.htm
Type of tail fin where the lower lobe is the longer and is supported by the vertebral column. Asymmetrical externally as well as internally
Formen present on the ectepicondyle of the humerus.
Tail fin in which the the caudal part of the notochord tapers posterodorsally. Based on Pradel et al. 2007
Osteostracans are the only jawless vertebrates that share with gnathostomes an epicercal tail.
Caudal fin lepidotrichium located upon or above the notochord.
Posteriorly projecting bony tubercle that is located proximal to the lateral condyle of the femur.
A small plate of cartilage synchondrotically united with the pubis. Modified from Baez and Harrison 2005.
The vertical plate of bone or cartilage attached to the median line of the sternum. Modified from Baumel et al. 1993
An enlarged ossified keel is found in most, but not all, volant birds.
An opening in the dermal armour of basal gnathostomes that encloses the pectoral fins. (modified from Young 2010).
Disjoint from 'pectoral fenestra' of Amphibians (AAO_0000779).
Distinct posterior most of the two 'double heads' of the blade of the ilium.
A notch for the articulation of the clavicle on other girdle elements.
It spresences gives the ilium a 'double headed' appearence.
A bony projection on the lateral side of the tibia, allowing contact between the later and the fibula.
Zone of bone organ located on the flat ventral side of the distal region of the furcula, serving as attachment region for pectoral muscles.
Centrale in the postaxial region of the mesopodium.
The paried limbs have a main axis running proximodistally trough the stylopodiam element (humerus/femur). from the zeugopodium distally elements can be divided into preaxial (on the radius/tibia side) and postaxial (ulna/fibula) sides. The exact orientation of these axises vary depending on the orientation of the limb in a neutral position.
Centrale in the preaxial side of the mesopodium.
The scapula's contribution to the glenoid fossa.
replaced by 'pars glenoidalis of scapula'
A constricted region of the ilium which is dorsal to the acetabulular region. Prior to the expansion of the iliac blade.
Bony projection that is part of the dorsal surface of the ischim, where it articulates with the ilium.
Bony projection that is part of the dorsal surface of the pubis where it meets the ilium.
Articular surface on calcaneum for the fibula.
Articular surface on the astragalus for the fibula.
Region consisitng of the ethmoid and sphenoid bones.
Eminence on the proximo-dorsal surface of the ungual, for attachment of flexor muscles.
The medial most digit of the manus skeleton.
In most taxa this is digits II-IV, but this varies based on the number of digits and thier identity in the taxa examined.
Process on infraspinous (region below the spine) of scapula.
The deep fossa between the femoral condyles in which the cruciate ligaments are attached. From Medilexicon.com
Spine ventrally located on the body and not part of the pectoral, pelvic or anal fins.
Expansion of the distal region of the ischium.
The most lateral of the paired series of extrascapular bones and is the bone where the intersection of the otic, postotic and extrascapular or supratemporal canals occur.
A bony process on the dorsal side of the proximal region of the humerus which corresponds to the insertion site of the Latissimus dorsi muscle.
Muscle that represents one branch of the larger triceps brachii, origination site near the glenoid fossa on the scapula.
Dermal armour plate that is situated behind the head and constitute the dorsal most portion of the dermal shoulder girdle. Modified from Brazeau 2009, Young 2010
The medial of the the paired series of extrascapular bones which carries the extrascapular or supratemporal canal.
Pits located on the proximodorsal part of metacarpals denoting the attachemnt sites for ligaments.
Opening and/or passageway for nerve(s) in bone.
A distinct region on a skeletal element that demarcates the attachment area of a muscle or tendon. Often associated with rugosity or tubercles.
While this term is applicable to both vertebrates and invertebrates, the qualities used to demarcate muscle attachment areas between the two groups may not be identical.
Process located on the ventral shaft of the ischium that denotes the attachment site of the pubio-ischio-femoralis externus.
In birds the pubio-ischio-femoralis externus is sometimes called the M.oburatorius lateralis and medialis.
In most taxa this is digits I and V, but this varies based on the number of digits in the manus
In most taxa this is digits I and V, but this varies based on the number of digits in the pes.
Spine located anterior to the pectoral fin
Spine located anterior to the pelvic fin and posterior to the pectoral fin.
A triangular, anteroventrally facing area developed between the preaxial margin of the humerus and the proximal limb of the ventral humeral ridge. Based on Callier et al. 2009
Elongate process forming the anteriormost part of the pubis.
An skeletal element of the upper pectoral girdle overlapped by the opercular and posttemporal bones.
Slender bone connected to the carpus in pterosaurs. The bone, which may have pointed forward, supports the propatagium, a membrane located between the carpus and pectoral region.
This structure is unique to pterosaurs. There is debate wherther this structure is derived from metacarpal I, the carpal bones or is a a novel bone. See Unwin et al. 1996
Anteroposterior expansion of the distal region of the pubis.
Bony projection on the anterior portion of the ilium, anterior to the acetabulum that articulates with the pubis.
Contact zone between the pubis and the ischium.
A broad expnase of bone incorperating both the pubis and the ischium. Origin site for ventral limb muscle including the pubioishciofemoralis externus. Modified from Romer 1956
Originates from the puboischaidic plate and inserts on the hindlimb. Acts to adduct the hindlimb. Is anterior to cloacal gland in males. Modified from De luliis and Pulera.
Originates in on the pubic cartillage and inserts on the tibia, acts to adduct the hindlimb. Modified from De luliis and Pulera.
The dorsal extension of the scapulocoracoid above the level of the glenoid region in basal gnathostomes. Modified from Brazeau 2009.
Anatomical projections that are elongate processes in the mid and posterior regions of the sternum.
Anatomical projection (crest) located dorsaly to the acetabulum.
Bony rim that is part of the supraacetabular region.
The route through which structures pass between the base of the neck and the posterior scapular region. It is formed by the suprascapular notch of the scapula and the superior transverse scapular ligament. From http://medical-dictionary.thefreedictionary.com/suprascapular+foramen
Series of fused cervical vertebrae or vertebral elements. Based on Jeffrey C. Carrier. Biology of Sharks and Their Relatives, 2012. CRC Press.
'The synarcual is a structure incorporating the anterior vertebrae of the axial skeleton and occurs in vertebrate taxa such as the fossil group Placodermi and the Chondrichthyes (Holocephali, Batoidea)' DOI 10.1007/s00435-012-0169-9
Axial subdivision that includes a series of fused cervical vertebrae or vertebral elements. Based on Jeffrey C. Carrier. Biology of Sharks and Their Relatives, 2012. CRC Press.
Facet for the articulation of the tibia on the astragalus (talus).
Anatomical projection on the anterolateral region of the proximal end of the femur.
In Archosaurs was originally a possible insertion site for the m. iliofemoralis externus (Hutchinson 2001). In more derived dinosaurs this becomes a distinct process possibly providing the attachment surface for mm. iliotrochanteri in addition to m. iliofemoralis externus (Carrano and Hutchinson 2002)
Eminence or swelling on anatomical surface.
A ridge or similar projection rising above the surface of an anatomical structure.
A part in the body of an organism that corresponds to an opposite symmetrical part.
A transverse flattened or cylindrical plate in the posterior body wall opposite the anterior ends of the pelvic fins, in front of the vent and at the posterior end of the body cavity, that supports a few anterior pelvic radials and a basal cartilage, the basipterygium. from Leonard J. V. Compagno. 2001. Sharks of the World: An Annotated and Illustrated Catalogue of Shark Species Known to Date. Volume 2.
Potentially homologous to the pelvic girdle.
Endochondral element that is part of the suspensorium sometimes ossifying distally as the quadrate bone and linking the basal section of the braincase to the lower jaw.
The palatoquadrate cartilage is the primary element of the suspensorium in larval amphibians and can ossify distally in some taxa, becoming the quadrate bone. In mammals the quadrate bone becomes the incus.
Is a endochondral element that is part of the mesopodial skeleton and is contained within the prepollex which in some taxa appears as a pre-axial digit-like projection anterior to the first digit of the hand.
Is a endochondral element that is part of the mesopodial skeleton and is contained within the prehallux which in some taxa appears as a pre-axial digit-like projection anterior to the first digit of the foot.
Foramina found on the humerus of tetrapodomorphs beyond the entepicondyle and ectepicondyle foramen. Often denoted as foramen 'c' and 'd' after Jarvik 1996
A collection of attached ridges on the ventrl surface of the femur consisting of the internal and fourth trochanters plus the adductor blade and crest. Most notible in early amniotes (based on Romer 1956)
The median series of bones supporting the pectoral fin of sarcopterygian fish. See Dipnomorpha. In the pectoral fin, the first mesomere is the humerus, the second the ulna, and the third probably the intermedium. The radius is the first preaxial radial. All other homologies are suspect. from http://palaeos.com/vertebrates/glossary
A scute parte of the basal surface of the fin in Sarcopterygian fish
The space between the bones of the tibia and the fibula.
Process on the humerus of basal tetrapods, anterior to the entepicondyle and associated with subscapularis muscle (based on Coates 1996)
Process on the humerus of basal tetrapods, anterior to the entepicondyle (see Coates 1996)
The area encompassing the radial and ulnar condyles of the humerus.
A bony dorsal extension of the clavicle.
The moon shaped fusion of distal carpals 1 and 2 found in some theropod dinosaurs, permitting greater wrist mobility.
The region of the astragalus/ talus that carries the articular surface for the navicular.
The rough eminence which is on the anterior inner aspect of the neck of the radius and into which the tendon of the biceps is inserted. From http://www.merriam-webster.com/medical
his roughened area of bone sits distomedially at the base of the coronoid process. It is the attachment site for the brachialis muscle. From http://www.anatomyexpert.com/
A fossa on the distal humerus proximal to the entepicondyle.
Increase the number of phalanges per digit beyond their ancestral digital formulas. Modified from Cooper and Dawson 2009
This class was obsoleted as it did not represent an anatomical structure
An articular process on anterior surface of neural arch of vertebrae which fits into zygantrum. Modifued from Henderson's dictionary of Biological terms 12th Edition.
zygosphene
ulnar facet of the humerus
Anatomical project part of the blade of the ilium that projects posteriorly.
posterodorsal process of ilium
The anteriormost of the two possible elements found in the tetrapod centrum (when the centrum is not a single element).
If there is only one element that makes part of the centrum it can be either the intercentrum (some amphibians) or the pleurocentrum (amniotes) (see Hildebrand and Goslow 's Analysis of Vertebrate structure)
intercentrum
The posteriormost of the two possible elements found in the tetrapod centrum (when the centrum is not a single element).
pleurocentrum
The intercentrum unit of the atlas vertebra.
Ridge or keel at the proximal end of the humerus. (see Laurin 1998)
anterior humeral ridge
Process that is part of the mandible that is in close proximity to the incisor teeth.
incisor process
Ciliary restraint system in the inner ear that uses sallets instead of the tectorial membrane.
sallet sensory system
Facet on the ulna for articulation with the ulnar condyle of the humerus.
humeral facet on the ulna.
Facet on the radius for articulation with the radial condyle of the humerus.
humeral facet on radius
The internal part of the rim denoting the coracoid foramen.
internal rim of coracoid foramen
the external wall of the rim denoting the coracoid foramen.
external rim of the coracoid foramen
Radial bone found in between the proximal and distal radial bones.
pectoral fin intermediate radial bone
A projection on the postaxial region of the ulnare.
postaxial process of the ulnare
A projection on the postaxial region of the femur.
postaxial process of the femur
A projection on the postaxial region of the fibula.
postaxial process of the fibula
pectoral process of humerus
deltoid process
Facets for the articulation of the epipodial (zeugopodial) elements.
Line of junction between two parts immovably connected. Modified from Henderson's Dictionary of Biological Terms.
suture
fibula facet of femur
tibial facet of femur
A collection of muscle and tendinous tissue.
musculotendinous bundle
middle phalanx of manual digit 1
iliac ramus
Distinct layer that indicate the growth of an organism.
growth line
Groove along the distal margin of the humerus, ventral to the radial and ulnar condyle.
distal groove of humerus
Foramen located on the scapulocoracoid, located just behind the cleithral anteroventral process(the articulation with the cleithrum). Modified from Coates 1996
foramen C
Modified from Garvey et al. 2005. " Between the dorsal ridge and the caput humeri is a futher recessed area......that clearly separates the two structures and is slightly separted from the dorsal surface of the entepicondyle, and more specifically from the unfinished bone of the entepicondyle, by a narrow ridge."
columnar area
Muscle found primarily in basal sarcopterygians that runs between teh scapulocoracoid and the humerus. Its exact homologies with more derived shoulder muscles in Tetrapoda is unclear.
scapulohumeralis muscle
A ramus of the celithrum that descend along the girdle. Its rounded outer surface forms the articulation surface for the clavicle while its anterior surface overlaps with the anterior process of the scapulocoracoid.
anteroventral process of cleithrum
excurrent foramen of ectepicondylar foramen
incurrent foramen of ectepicondylar formen
An anatomical surface that is part of a bone
surface of bone
A bone surface that is not smooth and periosteal. The usual implication is that the bone was still growing, was covered in cartilage, or both. From Paleos.com
unfinished bone surface.
finished bone surface
A process, extending dorsally from the clavicular plate, that attaches to the cleithrum. Modified from Clack 2012 and Coates 1996.
dorsal clavicular process
precoronoid bone
postcoronoid bone
anterior coronoid bone
posterior coronoid bone
coronoid fang
shagreen tooth field
fronto-ethmoidal shield
postrostral bone
median postrostral bone
...a v-shaped pair of ridges, each carrying three or four smallpores Modified from Ahlberg et al. 2005
surangular pit line
anterior supraorbital bone
Bone, often with tooth attachments, on the lingual side of the anterior of the lower jaw.
parasymphysial plate
mesial parasymphysial foramen
lateral parasymphysial foramen
Region of the endocranium that encompasses the connection between the hypothalamus and the anterior pituitary.
hypophysial region
The ossification of the Meckel's cartilage.
meckelian bone
meckelian foramen
A fossa that is a depression in the proximal end of the maxilla involved in articulation with the palatine. [Baldwin, CC and Johnson GD. 1996. Interrelationships of Aulopiformes. Pages 355-404 in MLJ Stiassny, LR Parenti, and DG Johnson, (eds.), Interrelationships of fishes. Academic Press, San Diego, CA.]
A process on the palatine that projects outward and upward and articulates with a depression (maxillary saddle) in the proximal end of the maxilla. [Gosline WA et al, 1966; Baldwin, CC and Johnson GD. 1996. Interrelationships of Aulopiformes. Pages 355-404 in MLJ Stiassny, LR Parenti, and DG Johnson, (eds.), Interrelationships of fishes. Academic Press, San Diego, CA.]]
Paired, thin dermal bones at the rear of the caudal fin skeleton, derived from scales.
A continuous flap of skin with scales implanted in pockets or invaginations. [Baldwin, CC and Johnson GD. 1996. Interrelationships of Aulopiformes. Pages 355-404 in MLJ Stiassny, LR Parenti, and DG Johnson, (eds.), Interrelationships of fishes. Academic Press, San Diego, CA.]
The space in the pupil, which is not occupied by the lens. A rostral aphakic space may enhance the forward binocular field of vision.
A series of scales in alignment with each other along some axis of the body. [PHENOSCAPE: bf].
Process that is posteriorly oriented and medially located on the basipterygium. It is a paired projection. [PHENOSCAPE:bf]
Anatomical cluster that consists of the epipleurals. [PHENOSCAPE:bf]
A rudder-like lobe formed from extensions of dorsal and anal fin rays.
Found in ocean sunfishes (Molidae) which lack a caudal fin. TODO: consider relationship to fin.
According to Forey 1988, History of the Coelacanth fish: 'In placoderms there are large overlapping plates which completely encircle the body and superficially may be matched with those in osteichthyans (Stensio, 1959; Forey, 1980; Jarvik, 1980). Thus, the anterior median ventral, anteroventral and anterior lateral of placoderms lie in the same positions as the interclavicle, clavicle (ventral cleithrum) and cleithrum (dorsal cleithrum) of osteichthyans.'
Cartilage element associated with the pelvic fin in aulopiform fishes.
Paralepidids (except Anotopterus), Alepisaurus, and evermannellids have a well-developed cartilage that extends dorsally into the body musculature from the region where the lateral pelvic-fin rays articulate with the girdle. In some young specimens, this cartilage is attached by a small rod of cartilage to the cartilage capping the central process, suggesting that it originates as part of the lateral cartilage. A similar cartilage is present in myctophids (Fig. 4A) but lacking in other aulopiforms and outgroups. [From Baldwin CC & Johnson GD (1996) Interrelationships of Aulopiformes. Interrelationships of Fishes, eds Stiassny MLJ, Parenti LR, & Johnson GD (Academic Press, San Diego, CA), pp 355-404.]
Dermal bone formed by the fusion of dermethmoids and rostral bones. [Fink, W L Weitzman, S H. 1982. Relationships of the stomiiform fishes (Teleostei), with a description of Diplophos Bulletin of The Museum of Comparative Zoology 150:31-93. http://www.biodiversitylibrary.org/part/28697]
In the clasper skeleton, a flat semicylindrical cartilage that is partially fused to the lateral edge of the axial cartilage, and forms the lateral wall of the clasper groove. [Compagno, L. 2001. Sharks of the World: An Annotated and Illustrated Catalogue of Shark Species Known to Date. Volume 2]
The large cartilage of the dorsal fin, on which the radials articulate distally. [Compagno 2001. Sharks of the World: An Annotated and Illustrated Catalogue of Shark Species Known to Date. Volume 2]
The large cartilage of the anal fin, on which the radials articulate distally. [Compagno 2001. Sharks of the World: An Annotated and Illustrated Catalogue of Shark Species Known to Date. Volume 2]
Dermal bone that is part of the scapular complex in placoderm fishes.
Dermal bone that is part of the scapular complex in placoderms.
Dermal articulation between skull and shoulder girdle localized to paired dermal neck-joint between anterior dorsolateral plate (ADL) and paranuchal (PNu) plates in placoderms.
TODO: add ADL and PNu classes and relationships
Membrane that connects the lepidotrichia or ceratotrichia of a fin.
The large cartilage of the posterior dorsal fin, on which the radials articulate distally.
The large cartilage of the anterior dorsal fin, on which the radials articulate distally.
Cartilage element on the neurocranium of sawsharks and batoids, separate cartilages attached to the sides of the nasal capsules that support the sides or front of the head. [Compagno, L.J.V. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. Volume 2. Bullhead, mackerel and carpet sharks (Heterodontiformes, Lamniformes and Orectolobiformes). FAO Species Catalogue for Fishery Purposes. No. 1, Vol. 2. Rome, FAO. 2001. 269p. ISBN 92-5-104543-7]
Endochondral element that is median and located in the dorsal skeletogenous septum between the cranium and the dorsal fin.
Fin ray that is composed of bone tissue.
A small smooth area on a bone or other firm structure. A worn spot on a tooth, produced by chewing or grinding.
mesopterygium element
metapterygium element
propterygium element
mesopterygium bone
metapterygium bone
propterygium bone
The x bone is a detached neural spine anterior to the neural spine of preural centrum 2.
In fishes, accessory bones (e.g., X bone) are common in Gadiformes and rare in Zeiformes (Borden et al., 2013).
The y bone is a detached neural spine anterior to the haemal spines of preural centrum 2.
Comment: In fishes, accessory bones (e.g., Y bone) are common in Gadiformes and rare in Zeiformes (Borden et al., 2013).
Anal fin pterygiophore that is the anteriormost of the series.
Anal fin spine that is the anteriormost element of the series.
Anal fin spine that is located posteriorly adjacent to the first anal fin spine.
A small to large enameloid-covered, dentine-cored spine located on the anterior margins of one or both of the dorsal fins, found on bullhead sharks (Heterodontiformes), many dogfish sharks, fossil (but not living) batoids, chimaeroids, but lost entirely or buried in the fin bases of other shark-like fishes. [def from Compagno, Sharks of the World]
Scale that is posteriorly adjacent to the pectoral girdle. [Cloutier and Arratia 2004, character 183]
postcleithral scale
Pectoral fin lepidtrichium that is small, unbranched and unsegmented.
A paired dermal bone in Gasterosteiformes connected with the coracoid and extending posteriorly. Has also been applied to the element below the scapula and applied to the coracoid in Dipnoi. Dictionary of Ichthyology.
Caudal vertebra that is the anteriormost element of the series.
Zone of bone organ that is the ventral extension of the posttemporal.
Zone of bone organ that is part of a lepidotrich and connected to other segments by collagen fibers. These segments lend flexibility to the lepidtrich.
Lepidotrichial segment that is part of the proximal region of a caudal fin ray.
Endochondral element that separates the olfactory region from the orbit, extends medially to meet its fellow medially below the frontal bones and is bordered by the mesethmoid anteriorly. It may articulate with the autopalatine and infraorbital 1 laterally. The lateral ethmoid is paired.
Lepidotrichial segment that is part of the distal region of a caudal fin ray.
An adhesive disk modified from the pelvic fins in, for example, clingfishes (Gobiesocidae), gobies (Gobiidae) and snailfishes (Liparidae).
pelvic sucking disc
Distinctive first dorsal fin taking the form of a modified oval sucker-like organ with slat-like structures that open and close to create suction and take a firm hold against the skin of larger marine animals.
For discussion of the homology of the sucking disc and dorsal fin, see Britz and Johnson (2012) (DOI: 10.1002/jmor.20063).
Soft ray that is part of the dorsal fin.
Soft ray that is part of the pelvic fin.
Region surrounding the glenoid fossa on the scapulocoracoid. [PHENOSCAPE:AD]
Region of dorsal fin that is composed of spinous rays (vs soft rays). [PHENOSCAPE:LJ]
A fossa on the posterior median part of the neural arch of a vertebra (as of a snake) that accommodates the zygosphene of the next vertebra. [PHENOSCAPE:JL]
Anatomical region lying to the anterior or dorsal side of the metapterygial axis. [PHENOSCAPE:AD]
The intercentrum unit of the axis vertebra.
Ridge that is part of the ilium. [PHENOSCAPE:AD, WD]
Tectorial restraint system is a type of ciliary restraint system for hair cells in the inner ear. In tectorial restraint systems, the tectorial membrane restrains the cilia of the hair cells by attaching either directly to ciliary tufts or indirectly through various kinds of fibrous structure (simple fibers, fibrous strands, finger-like processes, tectorial plates). [Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. 1988. Eds. R Estes, GK Pregill. Stanford University Press]
Bony protuberance on the external surface of the occipital bone.[PHENOSCAPE:AD]
Elements of the sacrum joining true sacral vertebrae to pelvis. [12th edition of Henderson's Dictionary of Biological terms]
Cloacal glands that secrete into the dorsal roof of the cloacal tube and or the anterior cloacal chamber. Found in male salamanders.
Cloacal gland present in males that secrete into the dorsolateral walls of the cloaca (between dorsal pelvic gland and anterior ventral pelvic gland clusters). Found in salamanders.
Foramen for the passage of the glossopharyngeal nerve IX. [PHENOSCAPE:WD]
The region of the upper jaw on or near the midline. [PHENOSCAPE:WD]
Region of the braincase which bears the facets for the hyomandibula in fishes. This region disappears in the origin of tetrapods and the space it occipied comes to contribute to the fenestra vestibulii. Clack, JA, 2001. Ch. 23, The otoccipital region. In Major Events in Early Vertebrate Evolution. Per Ahlberg editor.
Tooth of the upper jaw that is adjacent to the upper jaw symphysis. [PHENOSCAPE:WD]
The region of an anatomical structure (such as a tooth or jaw bone) facing the tongue. [PHENOSCAPE:WD]
The region of an anatomical structure, such as a tooth or jaw bone, facing the lips.[PHENOSCAPE:WD]
The region of an anatomical structure, such as a tooth or jaw bone, oriented posteriorly and facing the lips.[PHENOSCAPE:WD]
The region of an anatomical structure, such as a tooth or jaw bone, facing the midline of the jaw.[PHENOSCAPE:WD]
Foramen for the passage of the internal carotid artery.
The posterior and innermost of the three principal basal cartilages in the fins of fishes.
Relevant to Elasmobranchii and Holocephali. It is usually the longest basal and is exceptionally long in males where it is distally modified into a clasper.
Elastoidin fin ray that is thickened, generally unbranched and found in the fins of Chondrichthyes.
A rod-like entity that functions in support of fin folds and fins
Fin ray that is composed of elastoidin, unmineralized, and unsegmented.
Fin ray found in dipnoans that are composed of a superficial region of acellular fibrous bone, and a deep, mostly unmineralized, zone (G�raudie and Meunier 1982)
From Witten & Huysseune (2007): 'Two zones have been recognized in these camptotrichia: a superficial region of acellular fibrous bone, and a deep, mostly unmineralized, zone (G�raudie and Meunier 1982).'
A subdivision of the autopod consisting of manual digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 1 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit 2 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 2 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit 3 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 3 ( phalanges plus metapodial) plus soft tissue
manual digit III plus metapodial segment
A subdivision of the autopod consisting of manual digit 4 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 4 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 5 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 1 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 2 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 2 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 3 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 3 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 4 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 4 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 5 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 1 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 2 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 2 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 3 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 3 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 4 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 4 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit 5 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit 6 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 6 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit 7 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 7 ( phalanges plus metapodial) plus soft tissue
manual digit VII plus metapodial segment
A subdivision of the autopod consisting of manual digit 8 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit 8 ( phalanges plus metapodial) plus soft tissue
manual digit VIII plus metapodial segment
A subdivision of the autopod consisting of pedal digit 6 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 6 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 7 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 7 ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of pedal digit 8 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
pedal digit 8 ( phalanges plus metapodial) plus soft tissue
pedal digit VIII plus metapodial segment
A subdivision of the autopod consisting of alular digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
alular digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual major digit (Aves) plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual major digit (Aves) ( phalanges plus metapodial) plus soft tissue
manual major digit (Aves) digitopodial subdivision
manual major digit (Aves) plus metapodial segment
A subdivision of the autopod consisting of manual minor digit (Aves) plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual minor digit (Aves) ( phalanges plus metapodial) plus soft tissue
manual minor digit (Aves) digitopodial subdivision
manual minor digit (Aves) plus metapodial segment
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 1 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element.
individual digit of digitopodial skeleton
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 2 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 3 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 4 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 5 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 1 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 2 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 3 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 4 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 5 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 1 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 2 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 3 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 4 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of digit 5 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 6 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 7 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 8 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 6 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 7 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 8 plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of alular digit plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual major digit (Aves) plus the associated metapodial element.
manual major digit (Aves) digitopodial skeleton
A subdivision of the skeleton of the autopod consisting of the phalanges of manual minor digit (Aves) plus the associated metapodial element.
manual minor digit (Aves) digitopodial skeleton
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
Notes on how instances of this class functon biomechanically.
Notes on the location, position or part-parents of instances of this class.
A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)
A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral condition
The range is currently non-negative integer
x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
gill arch N = PA N-2. the term branchial_arch is ambiguous.
x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.
The correct terminology is yet to be established; in tetrapods 'ray' might mean the mereological sum of the phalanges of a manual digit plus a metatarsal bone (or equivalent for hindlimb)
x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2
Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1
x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae.
In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals.
Note that in TAO, ribs are numbered by *vertebrae*
x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas).
x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite.
x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendage
x appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments).
Examples: in dropsphila coxa=1, trochanter=2, femur=3, tibia=4, tarsal segments 1-5=5-9, pretarsus=10
x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere.
x tooth_number N if and only if (i) x is a tooth, and (ii) x is ancestrally tooth number N in a series of teeth repeated along an anterior-posterior axis, typically on the lateral side of a structure such as a jaw, with tooth_number 1 being the anteriormost. Note that this count refers to the total number of teeth starting from the first, regardless of the type of tooth. If sub-systems are required for numbering within a series of teeth of the same type, consider a subproperty. For example, in a human, maxillary canine = tooth 3 of upper jaw = canine_tooth 1 of upper jaw
Syntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property.
FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
Sarah Whitcher Kansa - https://orcid.org/0000-0001-7920-5321
Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
ISBN-10:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall
ISBN-10:0443065837 Human embryology, Larsen
ISBN10:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis
ISBN10:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos
ISBN10:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher
ISBN10:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack
ISBN10:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber
ISBN:0030229073 Invertebrate Zoology, Barnes
ISBN:0683400088 Stedman's Medical Dictionary
ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody
ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte
ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader
ISBN:9780878932504 Developmental Biology
PMID:11433360 Placental development: lessons from mouse mutants
PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/ext.owl>))) [Axioms: 25099 Logical Axioms: 4744]
preferred term in the context of comparative anatomy
A historic synonym, no longer encouraged
a synonym made on the basis of a possibly homologous structure in another species
preferred term when talking about an instance of this class in Homo sapiens
indicates that a synonym is used in an inconsistent or confusing way, typically between species
synonym that is inappropriate for amniotes
synonym that is inappropriate for mammals
expert consultation and attribution required
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
x is a conduit for y iff y passes through the lumen of x.
brain region defined by cyto-architecture
classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology
A class which has a weakened disjointness axiom, to avoid inconsistency. These are kept separately in the uberon_disjoint_from_strict ontology.
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
Indicates that subclasses in AOs may be inappropriately linked
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
derived from the union of EHDAA2 and EMAPA - still to be checked
subset of classes that have logical defs text defs and synonyms aligned with FEED
Subset consisting of classes creating for grouping purposes
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
classes that have some inconsistency with FMA
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s
somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads
core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out
abstract class brought in to group ontology classes but not informative
organs, excluding individual muscles and skeletal elements
A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms
Indicates that the class encompasses classes from other AOs that have not been verified
abstract upper-level terms not directly useful for analysis
Terms in this subset group together terms from different anatomy ontologies that have conflicting upper ontology/CARO assignments. For example, in FMA the naris is immaterial and in ZFA it is an organism subdivision.
core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
A term classified differently in FMA due to its treatment of branching structures - to be reviewed and revised by editors
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431
DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.525
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625
DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
DOI:10.1017/S095252380623342X Ahnelt PK, Schubert C, Kübber-Heiss A, Schiviz A, Anger E, Independent variation of retinal S and M cone photoreceptor topographies: A survey of four families of mammals. Visual neuroscience (2006), http://www.ncbi.nlm.nih.gov/pubmed/11193946 Azuma N, Molecular cell biology on morphogenesis of the fovea and evolution of the central vision. Nihon Ganka Gakkai Zasshi (2000), DOI:10.1016/S1350-9462(00)00012-4 Ahnelt PK, Kolb H, The mammalian photoreceptor mosaic-adaptive design. Progress in Retinal and Eye Research (2000)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.553
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414
DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and p.58
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53 and p.413-414
DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)
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ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.342
PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
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not well differentiated from the cerebrum. (Ariens, p. 868)
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484
most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572
Lancelets possess a region similar to the hypothalamus (Murakami, 2005)
DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224
ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000)
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.336
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
DOI:10.1016/j.autneu.2010.03.002 Young HM, Cane KN, Anderson CR, Development of the autonomic nervous system: A comparative view. Autonomic Neuroscience : basic and clinical (2010)
DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.462
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3
ISBN:978-3899370805 Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48
DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)
DOI:10.1016/j.ddmec.2004.08.004 Haramis APG, Clevers HC, Holehearted: genetic approaches to congenital cardiac valve malformations. Drug Discovery Today: Disease Mechanisms (2004)
PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430
ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.256
ISBN:978-0471210054 Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.260-261
DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)
ISBN:978-0471210054 Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.272, DOI:10.1002/cne.22364 Volkmann K, Chen YY, Harris MP, Wullimann MF, Köster RW, The zebrafish cerebellar upper rhombic lip generates tegmental hindbrain nuclei by long-distance migration in an evolutionary conserved manner. The Journal of Comparative Neurology (2010)
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and Figure 12-15
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.33
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
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DOI:10.1007/s00427-004-0450-0 Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4)
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
DOI:10.1371/journal.pone.0003582 Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS ONE (2008)
DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256
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ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.193
PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)
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DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004)
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627
PMID:11581521 Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001), DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)
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ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
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ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.16-17
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ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
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does not quite work for some muscles such as stylopharyngeus
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ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998)
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ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474
PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
WBbt coelomocyte currently classified as circulating cell
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PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235, DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)
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PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636
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taken from version of VSAO used in TAO and used directly in Uberon
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ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3
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PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)
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ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27
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PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)
PMID:15817505 Warburton D, Bellusci S, De Langhe S, Del Moral PM, Fleury V, Mailleux A, Tefft D, Unbekandt M, Wang K, Shi W, Molecular mechanisms of early lung specification and branching morphogenesis. Pediatric Research (2005)
ISBN:978-0721676685 Romer AS, Parsons T, Vertebrate body (1977) p.105-106
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, DOI:10.1146/annurev.cellbio.17.1.255 Chow RL and Lang RA, Early eye development in vertebrates. Annual Review of Cell and Developmental Biology (2001)
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ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331
DOI:10.1387/ijdb.072470fc The spatio-temporal pattern of testis organogenesis in mammals - insights from the mole. The International Journal of Developmental Biology (2009)
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ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333
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