Michel Dumontier
Semanticscience Integrated Ontology (SIO)
use,share,modify,commercial; by attribution [http://creativecommons.org/licenses/by/3.0/].
Contributors are those that engage in discussions in the context of SIO (in alphabetical order): christopher baker joachim baran jerven bolleman alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong luke mccarthy jim mccusker jose miguel cruz-toledo robert hoehndorf simon jupp jin-dong kim dana klassen james malone chris mungall david osumi-sutherland nuria queralt alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales
The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology
general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in'
is related to
A is related to B iff there is some relation between A and B.
'is related to' is the top level relation in SIO
has attribute
has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.
is attribute of
is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.
denotes
denotes is a relation between an entity and what it is a sign or indication of, or what specifically means.
the symbol '%' denotes a proportion in relation to a whole.
has part
a collection of cars has as a car as a part;a car has an engine as a part; a car has a piston as a part;
has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part.
is time boundary of
has proper part
a car has an engine as a proper part; a car has a piston as a proper part;
has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part.
has boundary
has boundary is a mereological relation between a whole and boundary located at its periphery.
the surface of an apple is a 2D boundary of the apple.
has member
a collection of cars has as a car as a member
has member is a mereological relation between a collection and an item.
is denoted by
is located in
A is located in B iff the spatial region occupied by A is part of the spatial region occupied by B. [T][R]
A parasite in the interior of a person's intestine is located in their intestinal lumen.
is participant in
a car is a participant in a car race; glucose is a participant in glycolysis
is participant in is a relation that describes the participation of the subject in the (processual) object.
is agent in
hexokinase is an agent in the conversion of glucose to glucose-6-phosphate
is agent in is a relation between an entity and a process, where the entity is present throughout the process, no permanent material change occurs, and is a causal participant in the process.
sadi
is provider of
is provider of is a relation between a source and the entity it makes available.
has provider
is provided by is a relation between an entity and the entity that provides it.
is part of
is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole.
is proper part of
is proper part of is an asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.
is member of
is member of is a mereological relation between a item and a collection.
is boundary of
is boundary of is a mereological relation between a boundary located at the periphery of a whole.
is contained in
A is contained in B iff the spatial region occupied by A is part of the spatial region occupied by B and A is not part of B. [T]
has participant
has participant is a relation that describes the participation of the object in the (processual) subject.
has agent
has agent is a relation between a process and an entity, where the entity is present throughout the process and is a causal participant in the process.
is location of
A is location of B iff the spatial region occupied by A has the spatial region occupied by B as a part. [T][R]
contains
A contains B iff the spatial region occupied by A has the spatial region occupied by B as a part, and B is not part of A. [T]
is connected to
A is connected to B iff there exists a fiat, material or temporal path between A and B. [S][T]
is adjacent to
A is adjacent to B iff there is a small, but non-zero distance between A and B
is represented by
is represented by: a relation between an entity and some symbol.
is supported by
is supported by is a relation between a proposition and something that supports the truth of the assertion.
is disputed by
has disputing evidence is a relation between a proposition and something that disputes (does not directly support) the truth of the assertion.
is supporting evidence for
is disputing evidence for
represents
a represents b when a serves as a sign, symbol or model of b.
is positionally after
is positionally after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity.
is referred to by
A is referred to by B iff B is an informational entity that makes reference to A.
has concretization
A has concretization B iff A is an informational entity and B is the a quality of some material entity.
is concretization of
A is concretization of B iff A is a quality of a material entity and B is an informational entity.
is measurement value of
is measurement value of is a relation between a value and the entity that it is a measurement of.
has measurement value
has measurement value is a relation between a quality/realizable and a measurement value.
has quality
has quality is a relation between an entity and the quality that it bears.
is quality of
is quality of is a relation between a quality and the entity that it is a property of.
is source of
is source of is a relation between a source of information about some entity.
has unit
has unit is a relation between a quantity and the unit it is a multiple of.
is unit of
is unit of is a relation between a unit and a quantity that it is a multiple of.
has property
has property is a relation between an entity and the quality, capability or role that it and it alone bears.
michel's hair has the quality of being brown in colour.
is property of
is property of is a relation betweena quality, capability or role and the entity that it and it alone bears.
has function
has function is the relation between an entity and a function that is ascribed to it.
is function of
is function of is a relation between a function and an entity that it is a property of.
is role of
is role of is a relation between a role and the entity that it is a property of.
has role
has role is a relation between an entity and a role that it bears.
has output
has output is a relation between an process and an entity, where the entity is present at the end of the process.
has input
has input is a relation between a process and an entity, where the entity is present at the beginning of the process.
is input in
glucose and ATP are inputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
is input in is a relation between an entity and a process, where the entity is present at the beginning of the process.
is output of
glucose-6-phosphate and ADP are outputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
is output of is a relation between an entity and a process, where the entity is present at the end of the process.
is implementation of
is implementation of is a relation between an information entity and a specification that it conforms to.
has implementation
has implementation is a relation between a specification and an implementation that conforms to it.
has disposition
has disposition is the relation between an entity and a disposition that it bears.
is disposition of
is disposition of is a relation between a disposition and the entity that it is a property of.
is positionally before
is positionally before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity.
is directly after
is directly after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity, and the entities are adjacent to one another.
is directly before
is directly before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity, and the entities are adjacent to one another.
is causally related with
A transitive, symmetric, temporal relation in which one entity is causally related with another non-identical entity.
is derived from
A transitive temporal relation in which one entity was materially formed from another non-identical entity.
derives into
a derives to b if and only if a or some part thereof is consumed in the formation of b.
immediately derives into
a immediately derives into b if and only if a or some significant part thereof is consumed in the formation of b and there are no identifiable intermediate entities between a and b.
is immediately derived from
A non-transitive temporal relation in which one entity is immediately derived from a non-identical entity such that there are no intermediate entities between them.
precedes
A transitive, temporal relation in which one process precedes (has occured earlier than) another process.
is preceded by
immediately precedes
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.
is immediately preceded by
A non-transitive temporal relation in which one process is immediately preceded by another process, such that there is no interval of time between the two processes.
is referenced by
is reference for is a relation between a document that provides information about an entity.
has source
has source is a relation between an entity and another entity from which it stems from.
is annotation of
is annotation of is a relation between some textual entity and the entity that it annotates.
has annotation
document x is annotated with the keywords 'ontology','semantic web'
has annotation is a relation between an entity and some textual anntotation.
is annotated with
was annotated with
is variant of
is variant of: a relationship indicating that two entities are different (by some measure), but either achieve the same objectives in different ways or are permutations of one another (temporal, logical or otherwise)
has direct part
a car has an engine as a direct part
has direct part is a relation to specify a part at a particular level of granularity
is prior version of
A is prior version of B iff A is a variant of B and B derives from A.
cites
cites is a relation to refer to by way of example, authority or proof.
is cited by
is cited by is a relation from an object that is referred to by way of example, authority or proof.
is similar to
is similar to is a relation between two entities that share one or more features.
is subsequent version of
A is subsequent version of B iff A is a variant of B and A derives from B.
is covalently connected to (transitive)
has target
has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process.
is target in
glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
is target in is a relation between an entity and a process, where the entity is present at the beginning of the process and undergoes a change or transformation in the process.
is weakly interacting with (transitive)
is weakly interacting with is a symmetric relation between two molecular entities (or any part thereof) that are interacting through some weak force (van der waals, hydrogen bonds, electrostatic interactions)
is causally related to
a is causally related to b iff there is a causal chain of events from a to b
is direct part of
is direct part of is a relation between a specific part (at some level of granularity) and its whole.
is product of
glucose-6-phosphate is the product of the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
is product of is a relation between an entity and a process, where the entity is present at the end of the process as a result of a transformation in the process target.
has product
has product is a relation between an process and an entity, where a new entity exists at the end of the process.
is component part of
is component part of is a relation between a component and a whole, where the component is instrinsic to the whole, and loss of the part would change the kind that the whole is.
is spatiotemporally related to
A is spatiotemporally related to B iff A is in the spatial or temporal vicinity of B
is surrounded by
A 'is surrounded by' B iff the A 'is contained by' B and A 'is adjacent to' B or A 'is directly connected to' B.
surrounds
A 'surrounds' B iff the A 'contains' B and A 'is adjacent to' B or A 'is directly connected to' B.
overlaps with
A overlaps with B iff there is some C that is part of both A and B. [S][R]
is about
is about is a relation between an information content entity and the entity that its primary subject.
is covalently connected to
is covalently connected to is a relation between an atom and another atom.
is weakly interacting with
specifies
A relation between an information content entity and a product that it (directly/indirectly) specifies
is specified by
a relation between a product and the information content entity that specifies it.
is manifested as
is manifested as is a relation between an expression and its manifestations.
the english language version of 'war of the worlds' is manifested as a collection of english language versions of the book.
is causally related from
a is causally related from b iff there is a causal chain of events from b to a
realizes
realizes is a relation between a process and a realizable entity (role, function, disposition).
is realized in
the role of a patient is realized in medical examination
satisfies
satisfies is a relation between an entity and the specification or objective that it conforms to.
is satisfied by
has creator
has creator is a relation between an entity and that which created it.
is created by
was created by
the iPhone was created by Apple Inc
is created by is a relation between an entity and its creator.
has component part
a human has blood as a component part
has component part is a relation between a whole and a component part where the component is instrinsic to the whole, and loss of the part would change the kind that it is.
has expression
the story 'war of worlds' is expressed as every language edition of the book 'war of the worlds'
is expression of
every language edition of 'war of the worlds' are expressions of the story of 'war of the worlds'
is expression of is a relation between more concrete expression of some conceptualization.
is broader than (t)
A is broader than B (t) iff for A is broader than B.
is narrower than (t)
A is narrower than B (t) iff for A is narrower than B.
is generically related with
A is generically related with B iff A is an abstract entity or an information content entity and B is a information content entity or a physical entity, respectively.
is manifestation of
is narrower than
A is narrower than B iff the meaning of term A is narrower in scope than the meaning of term B
is broader than
is match to
A is match to B iff A and B are terms with similar (related, broad, close, exact) meanings
is exact match to
is close match to
is broad match to
is dissimilar to
is dissimilar to is a relation between two entities in which one is considered dissimilar to the other based on some criteria.
is opposite to
hot is the opposite of cold; left is opposite of right
is opposite to is a relation between two entities in which one is diametrically opposed to the other.
is version of
is version of is a relation that holds between any two versions in which one is a subsequent or alternate version of (through a branch).
has parameter
has parameter is a relation between a process and an information content entity which modulates the behaviour of some participant.
is parameter in
is parameter in is a relation between a data item and some data transformation process.
is described by
is described by is a relation between one entity and another entity that provides a description (detailed account) of it.
is orthologous to
is orthologous to is a relation between two biological entities that share a common ancestor and occur in different species.
describes
describes is a relation between one entity and another entity that it provides a description (detailed account of).
has capability
SIO has the capability to semantically integrate data.
has capability is a relation between an entity and the capability that it bears.
refers to
refers to is a relation between one entity and the entity that it makes reference to.
is subject of
is paralogous to
is paralogous to is a relation between two entities which indicates their common ancestry as a result of a gene duplication.
references
references is a relation between one entity and the entity that it makes reference to by name, but is not described by it.
is model of
is model of is a relation between a model (an artifact) and the entity it purports to represent.
the architect builds a model that represents the building she envisions.
is modelled by
is xenologous to
a relation between two entities which indicates their common ancestry but due to horizontal gene transfer.
has trigger
has trigger is a relation between a realizable and the factor that causes it to be realized.
is trigger for
has basis
has basis is a relation between a realizable entity and the quality that forms the basis for it.
the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization).
is base for
is base for is a relation between a quality and the realizable entity that it is the basis for.
is realizable property of
has realizable property
is capability of
is capability of is a relation between a capability and the entity that bears it.
is directly connected to
A is directly connected to B iff there exists a path direclty between A and B.
transforms into
A transitive temporal relation in which an entity mainstains identity from one state to another.
immediately transforms into
A temporal relation in which an entity mainstains identity from one state to another.
is transformed from
is immediately transformed from
in relation to
in relation to is a comparative relation to indicate that the instance of the class holding the relation exists in relation to another entity.
has identifier
is identifier for
has unique identifier
has unique identifier is an inverse functional relation between an entity and an identifier that uniquely identifies it.
is unique identifier for
is unique identifier for is a relation between an identifier and an entity that it uniquely identifies
has time boundary
has start time
has end time
is start time of
is end time of
exists at
exists at is a relation between an entity and a time measurement.
is mutual disposition of
a is mutual disposition of b if and only if the realization of the disposition a necessarily causes the realization of the disposition b.
is greater than or equal to
is greater than or equal to is a comparison relation between two quantities in which the first has a value larger or equal to the second.
is mutually related to
a is mutually related to b if and only if the realization of the relation of a necessarily causes the realization of a relation to b.
is mutual role of
a is mutual role of b if and only if the realization of role a necessarily causes the realization of role b.
is lesser than or equal to
is greater than to is a comparison relation between two quantities in which the first has a value smaller or equal to the second.
is greater than
is greater than to is a comparison relation between two quantities in which the first has a value larger than the second.
is lesser than
is lesser than to is a comparison relation between two quantities in which the first has a value smaller than the second.
is comparable to
is comparable to is a relation between two entities that share at least one feature whose value can be compared.
is numerically comparable to
is numerically comparable to is a comparison relation between two quantities whose datatype value can be compared.
is equal to
is equal to is a comparison relation between two quantities whose value are exactly the same.
is inequal to
is inequal to is a comparison relation between two quantities whose value are not the same.
has evidence
has evidence is a relation between a proposition and something that demonstrates the truth of the assertion.
is evidence for
is refuted by
has evidence is a relation between a proposition and something that refutes (is incompatible with) the truth of the assertion.
is refuting evidence for
measured at
measured at is a relation between a measurement value and the time measurement.
in relation from
a in relation from b is a comparative relation in a is the object of reference in a relation with b.
has frequency
has frequency is a relation that specifies the occurence of an object or event
is frequency of
is frequency of is a relation between a temporal unit and an object or event
has substrate
has substrate is a relation between a process and an object where the object is destroyed by its participation in the process.
is first part of
is first part of is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
has first part
has first part is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
has last part
has last part is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
is last part of
is last part of is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
has ordered part
has ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
is ordered part of
is ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
is specialization of
a weather forecast for the city of London produced at a specific time is a specialization of a weather forecast for the city of London.
is specialization of is a relation between a more specific instance (in terms of spatial/temporal localization & other attributres) than the other.
is generalization of
is generalization of is a relation between a more general instance (in terms of spatial/temporal localization & other attributres) than the other.
is alternate of
two weather forecasts for the city of London produced at different times or by different organizations (etc) are alternates of each other, and instances of / specializations of forecasts for the city of London.
is alternate of relates two specialized instances.
is mutual capability of
a is mutual capability of b if and only if the realization of capability a necessarily causes the realization of capability b.
regulates
x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or extent of y
is regulated by
results in
is result of
affects
is affected by
is identical to
is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes.
is transitively related to
encodes
A relation between two objects, in which the first object contains information that is used to produce the second object.
an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology)
is encoded by
A relation between two objects, in which the first object is produced from the information contained in the second object.
is transcribed into
DNA is transcribed into RNA
a relation between two information content entities in which one is transcribed into (an exact or similar kind) another through some process.
is transcribed from
is translated into
RNA is translated into Protein
a relation between two information content entities in which one is translated into (a completely different kind of entity) another through some process.
is translated from
is homologous to
a relation between two entities which indicates their common ancestry.
has value
A relation between a informational entity and its actual value (numeric, date, text, etc).
entity
Every thing is an entity.
material entity
A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass.
quality
A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary.
process
A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.
social entity
A social entity pertains to the interaction among individuals and groups.
social structure
A social structure is a social entity which consists of relationships between two or more entities.
organization
An organization is a collective with a complex articulation of tasks, roles and responsibilities.
geographic position
A geographic position is the coordinate of an entity against some geographic coordinate system.
disposition
A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger).
solubility (to dissolve when put in fluid); fragility (disposition to break when dropped)
information content entity
information content entity is an object that requires some background knowledge or procedure to correctly interpret.
role
A role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance.
function
A function is a capability that satisfies some agentive objective, or (evolutionary) optimization.
site
A nostril; the interior of the heart valve; the interior of a bottle.
A site is a spatial region bounded (in part or in whole) by material entities and may be occupied by material entities.
material boundary
A material boundary is the boundary of a material entity which exists as a lower dimensional entity at exactly the location where its parts no longer extend into space. Every material entity has a boundary, and a boundary is the boundary of exactly 1 material entity.
the external surface of the window; the surface of the p52 protein
object quality
An object quality is quality of an object.
process quality
A process quality is quality that is associated with a process.
biopolymer sequence
A sequence is a primary structure descriptor in which each of the letters in the string represents a monomeric unit (residue) in which adjacent letters represent the connectivity between the monomeric units.
start date
A start date is a time instant pertaining to the date of the beginning of a process.
end date
An end date is a time instant pertaining to date of the end of a process.
process status
process status is a process quality that describes the state of a process.
completed
completed is that status of a process that successfully unfolds.
ongoing
ongoing is the status of a process that is not yet complete.
predicted
predicted is the quality of an entity that is thought to exist, as evidenced by some rational procedure.
spatial quantity
A spatial quantity is a quantity obtained from measuring the spatial extent of an entity
physical dimensional quantity
1D extent quantity
A quantity that extends in single dimension.
depth
depth is the dimensional extent into a plane of a 3D projection of the object.
height
height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference.
length
length is the longer dimensional extent along a 2D projection of the object.
width
width is the shorter dimensional extent perpendicular to a 2D projection of the object.
thickness
thickness is the shortest dimensional extent of a 3D projection of an object.
2D extent quantity
A quantity that extends in two dimensions.
area
area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane.
length of perimeter
A perimeter is a length of the outline that surrounds a two-dimensional shape.
circumference
circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius.
3D extent quantity
A quantity that extends in three dimensions.
volume
volume is the quantity of three-dimensional space enclosed by some closed boundary.
compositional quality
composition quality is a quality that describes its composition or anatomy.
quantity
A quantity is an informational entity that gives the magnitude of a property.
shape
shape is the quality of a bearer that relates to its spatial extent.
position
A measurement of a spatial location relative to a frame of reference or other objects.
orientation
orientation is an angle between the bearer and an axis, or the angle between the bearer and another object.
namespace
A namespace is an informational entity that defines a logical container for a set of symbols or identifiers.
data item
A data item consists of information that has been collected/generated towards some purpose.
measurement value
A measurement value is a quantitative description that reflects the magnitude of some attribute.
coordinate
A coordinate is a measurement of position in n-dimensional space.
cartesian coordinate
A Cartesian coordinate is the signed distance of a point to some referent line.
polar coordinate
A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction.
unit of measurement
A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.
mathematical entity
A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
plan
A plan is a set of intended actions, through which one expects to achieve a goal.
generic name
A generic name is the preferred name provided by manufacturer.
language entity
A language entity implements some language specification for the visual interpretation and is part of some document.
visual language entity
A visual language entity is a language entity that is expressed through physical expression of manual.
figure
A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities.
diagram
image
An image is an affine projection of a visual entity to a two dimensional surface.
depiction
photograph
A photograph is an image created by light falling on a light-sensitive surface.
photo
statistical graph
A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions.
question
A question is a linguistic expression used to make a request for information.
publication
A publication is a document that has been made available by a publisher.
record
A record is a document containing a collection of statements about some entity.
data set
A dataset is a data item that is a collection of data items.
specification
A specification is a description of the essential technical attributes/requirements for an object or procedure, and may be used to determine that the object / procedure meets its requirements/attributes.
action specification
An action specification is a specification composed of a sequence of instructions to achieve some objective.
biopolymer
A biopolymer is an organic polymer using biological components.
algorithm
An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function.
software entity
A software entity is a computational entity that can be interpreted by or directly executed by a processing unit.
software method
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
software module
A software module is software composed of a collection of software methods.
software library
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software application
A software application is software that can be directly executed by some processing unit.
software interpreter
A software interpreter is a software application that executes some specified input software.
software script
A software script is software whose instructions can be executed using a software interpreter.
language
Language is a language entity which is the result of encoding and decoding information through systematic creation and usage of systems of symbols, each pairing a specific sign with an intended meaning, established through social conventions
symbol
A symbol is a proposition about what an entity represents.
book
A book is a publication composed of a large number of entries.
chapter
A chapter is a document section of a book or thesis.
character
A character is a language symbol used to construct words.
novel
A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism.
paragraph
A paragraph is a self-contained unit of written discourse consisting of one or more sentences.
document section
A document section is a component of a document.
capability
A capability is a realizable entity whose basis lies in one or more parts or qualities and reflects possility of an entity to act in a specified way under certain conditions or in response to a certain stimulus (trigger).
sentence
A sentence is a grammatical unit consisting of one or more words that bear minimal syntactic relation to the words that precede or follow it.
word
A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language.
identifier
An identifier is a label that specifically refers to (identifies) an entity (instance/type).
name
A name is a label used to identify an entity.
preferred name
A preferred name is the name that is generally used by some organization.
common name
A common name is a name that is commonly used.
brand name
A brand name is a trademarked and marketed name of a product.
scientific name
A scientific name is a name given through scientific nomenclature.
magazine
A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports.
synonym
A synonym is a word with the same or very similar meanings.
antonym
An antonym is a word with opposite or nearly opposite meaning.
hypernym
A hypernym is a term with a broader meaning.
hyponym
A hyponym is a term with a narrower meaning.
homonym
A homonym is a word that sounds the same but has different meaning.
workflow
A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives.
ontology document
An ontology document is a document that contains an ontology.
pattern
A pattern is a generalized representation of some repeatable concrete or informational item.
sequence motif
A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein.
descriptor
A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document.
definition
A definition is a description that succintly characterizes an entity.
description
A description is language entity in which elements of a language (formal or natural) are used to characterize an entity.
category
A category is a class of entities having particular shared characteristics.
class
A class is a collection of sets which can be unambiguously defined by a property that all its members share.
web service
A web service is a software application that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.
criterion
A criterion is a specification to describe properties used for evaluation.
inclusion criterion
An inclusion criterion is a criterion that must be present to satisfy some objective.
exclusion criterion
An exclusion criterion is a criterion that must be absent to satistify the objective.
parameter
A parameter is variable whose value changes the characteristics of a system or a function.
monomer
A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer.
keyword
A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval.
document
A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate.
list
A list is any enumeration of a set of items.
manuscript
A manuscript is a document prior to publication.
note
A note is a brief document.
patent
A patent is an information entity granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.
article
An article is a publication that is stand-alone section of a larger work.
blog
A blog is a publication accessible at some website and is typically about various experiences.
book volume
A book volume is a book that is part of a collection.
conference proceedings
A conference proceedings is a book composed of papers presented at a conference.
book series
A book series is a collection of books that have been sequentially published.
edited publication
An edited publication is a publication that has been examined and potentially changed by an editor.
journal
A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published.
manual
A manual is a document that instructs on the usage of a device.
periodical
A periodical is a publication that appears on a regular schedule.
newspaper
A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising.
technical report
A technical report is a publication published by a school or other institution, usually numbered within a series.
thesis document
A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments.
honor's thesis
An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree.
master's thesis
A Master's thesis is a thesis prepared as a requirement for a Master's degree.
phd thesis
A PhD thesis is a thesis prepared as a requirement for a doctoral degree.
booklet
A booklet is a document that lacks a named publisher or sponsoring institution.
diary
A diary is a document which describes day-to-day experiences.
document component
A bibliographic attribute is an attribute related to publications.
address
An address is a position that indicates the physical location of some entity using a social convention.
affiliation
An affiliation is a social relation which indicates the partnership between two or more entities.
citation
A citation is a textual entity which denotes a source described in the bibliography or reference section of a document.
document title
A document title is a textual entity that summarizes the topic of the document in one sentence.
reference
A reference is a textual entity that describes a single source used in the preparation or development of the work.
page range
A page range denotes the start and end page in some document.
page total
A page total is a textual entity that is about the number of pages in some informational entity.
label
a label is a term that is associated with some entity
language label
A language label is a label that denotes the language of a textual entity.
first name
A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname.
last name
A last name (surname) is a name added to a given name and is part of a personal name and is often the family name.
personal name
A personal name is a name to identify an individual person and usually comprises of a first name and a last name.
legal name
A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate.
title
A title is a textual entity that summarily describes some entity.
document version
A document version is a version of a work in some sequence of derivative works.
abstract section
An abstract section is a document section that provides brief summary of a document that explains the main argument(s), topic(s) or findings.
acknowledgements section
An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work.
author contribution section
An author contribution section is a document section that describes the contribution of the authors.
author section
An author section is a document section that lists the contributing authors.
bibliography section
A bibliography section is a document section that is composed of a list of references used in the development of the work.
copyright section
A copyright section is a document section that contains a notice of copyright.
correspondence section
A correspondence section is a document section that contains the details for contacting the corresponding author.
discussion section
The discussion section is a document section containing a summary of the findings, a reflection on the significance of findings, comparison with related work, among others.
introduction section
An introduction section is a document section that generally provides background, motivation and goals of the work.
materials and methods section
The materials and methods section is a document section containing a description of the materials and methods used in the study.
materials section
The materials section is a document section containing a description of the materials used in the study.
methods section
The methods section is a document section containing a description of the methods used in the study.
results section
The results section is a document section describing the main findings of the study.
table of contents
The table of contents is a document section that lists all sections (and optionally subsections) in a sequential order along with their page number.
implies (->)
Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B.
namespace label
A namespace label is a short name for a namespace.
logical operator
A logical operator is a unary or binary relation to construct logical expressions.
conjunction (and)
AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false.
proposition
A proposition is a sentence expressing something true or false.
dimensionless quantity
A dimensionless quantity is a quantity that has no associated unit.
dimensional quantity
A dimensional quantity is a quantity that has an associated unit.
argument
An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion.
premise
A premise is a proposition of an argument from which the conclusion is drawn.
conclusion
A conclusion is a proposition which is reached after considering the evidence, arguments or premises.
deductive argument
A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises.
inductive argument
An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises.
sound argument
A sound argument is a valid argument with true premises.
valid argument
A valid argument is an argument where the truth of the conclusion is a logical consequence of the premises and (consequently) its corresponding conditional is a necessary truth.
invalid argument
An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises.
truth value
truth value is a quality of information that is claimed/verified to be true or false.
true
true is a truth value that indicates that it holds under all possible worlds.
false
false is a truth value in that indicates that it is not true.
term
A term is a word or phrase used to denote one or more entities.
emotion
An emotion is a process (experience) that arises internally or from an involuntary physiological response to a stimulus.
mass
mass is the quality of the amount of substance.
disjunction (or)
OR is a logical operator that results in true whenever one or more of its operands are true.
negation (not)
NOT is a logical operator in that has the value true if its operand is false.
exclusive disjunction (xor)
XOR, also called exclusive disjunction or (symbolized XOR, EOR, EXOR, or ⊕), is a type of logical disjunction on two operands that results in a value of true if exactly one of the operands has a value of true.
hypothesis
A hypothesis is a proposed explanation for a phenomenon.
academic organization
An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement.
social relation
A social relation is a social entity that describes a relationship between two or more individuals or groups.
set
A set is a collection of entities, for which there may be zero members.
university
A university is an institution of higher education and research which grants academic degrees in a variety of subjects and provides both undergraduate education and postgraduate education.
collection of documents
A collection of documents is a non-zero set of documents.
website
A website is a collection of documents published on the World Wide Web.
movie
A movie is a series of images that are displayed in rapid succession to give the impression of movement.
film
moving pictures
excerpt
An excerpt is a contiguous or discontiguous portion of a document.
quote
A quote is a excerpt that is attributed to a particular source.
geographic image
A geographic image is a photograph of some geographical area.
web page
A web page is a document that is published according to World Wide Web standards.
email
Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol.
process number
process number is a number associated with a process that denotes its ordinal position in a set of processes.
letter
A letter is a document that contains a personal communication from one part to another.
normality
normality is the quality in which the value may differ from normal or average
edition number
An edition number is count of a literary work edited and published, as by a certain editor or in a certain manner including being printed during some interval of time.
volume number
volume number is a count of a sequence of periodicals.
polymer
A polymer is a molecule composed of a connected set of monomeric residues.
functional specification
A functional specification is a specification that describes the characteristics of an object.
design specification
A design specification is a specification that provides precise and explicit information about the requirements for a product design.
spatial specification
A specification for spatial location is an effective specification towards representation spatial position or spatial data.
longitude
Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point.
latitude
Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane
coordinate system
A coordinate system is a specification for spatial location that uses a set of numbers, or coordinates, to uniquely determine the position of a point or other geometric element.
cartesian coordinate system
A Cartesian coordinate system specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.
concept
A concept is term that refers to a generalization of a set of attributes or entities.
polar coordinate system
A polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.
positional identifier
A positional description is a description of location using some system or frame of reference.
cylindrical coordinate system
A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis.
spherical coordinate system
A spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.
OWL ontology
An OWL ontology is an ontology as specified by the W3C OWL specification.
3D cartesian coordinate
A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate.
objective
An objective is a proposition that indicates a planned or anticipated outcome.
realizable entity
A realizable entity is an attribute that is exhibited under some condition and is realized in some process.
term variant
A term variant is a term that is a variant of another term.
to modify
to modify is the capability to change some entity.
to record
to record is the capability to detect and transcribe information in a specified format on some physical medium.
to magnify
to magnify is the capability to increase the appearance of the size of an object.
to heat
to heat is a capability to increase the internal kinetic energy of a material.
to cool
to cool is the capability to decrease the internal kinetic energy of a material.
to freeze
to freeze is the capability to decrease the internal kinetic energy of a material such that it changes state from a gas or liquid to a solid.
to separate
to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them.
to ionize
to ionize is the capability to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
to supply energy
to supply energy is the capability to transfer energy from a source to a sink.
to observe
to observe is the capability to watch attentively.
dysfunction
dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function.
fitness
fitness is the quality of an object with respect to some stated functions or evolutionary adaptation.
intent
intent is a desire to realize a particular outcome.
purpose
purpose is the reason for which something is done or created or for which something exists.
belief
A belief is a proposition that is believed to be true.
number
A number is a mathematical object used to count, label, and measure.
variable
A variable is a value that may change within the scope of a given problem or set of operations.
equation
An equation is a mathematical statement that asserts the equality of two expressions.
spatial region
A spatial region is an object contained in some region of space.
The airspace above Ottawa airport; the band around the northern hemisphere between 50 degrees N and 60 degrees N; the spatial region occupied by a bottle.
to measure
to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric.
to inject
to inject is the capability to administer a substance into some object through its external barrier.
to boil
to boil is the capability to increase the internal kinetic energy of a material such that it changes state from a solid or liquid to a gas.
to reduce energy
to reduce energy is the capability to remove energy from a source.
to supply electricity
to supply electricity is the capability to transfer electricity from a source to a sink.
to change materially
to change appearance is the capability to change the material composition of an object.
to demagnify
to demagnify is the capability to decrease the appearance of the size of an object.
to change appearance
to change appearance is the capability to change the visual attributes of an object.
perception
perception is the organization, identification, and interpretation of sensory information in order to fabricate a mental representation through the process of transduction, which sensors in the body transform signals from the environment into encoded neural signals.
to contain
to contain is the capability to bound or constrain a physical entity in some site.
to immobilize
to immobilize is the capability to contain an entity in such a way that it may not move in space.
to filter
to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through.
to excite
to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons).
to emit
to emit is the capability to release some physical entity (light, pollution, etc).
to change energetically
to change energetically is the capability to change the energetic aspects of an object.
to positively charge
to positively charge is the capability to remove an electron or add a positively charged ion to a chemical entity.
to negatively charge
to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity.
to assemble
to assemble is the capability to combine entities together into a larger object that persists in time.
to extract
to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain.
to transport
to transport is the capability to displace a material from one location to another.
time measurement
Time intervals are specified as date/datetime ranges.
the duration of my life; the duration of a surgical procedure, the moment of death
time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference).
to change spatially
to change spatially is the capability to affect the physical movement of some entity.
patient
A patient is an individual that is the recepient of medical care.
doctor
A doctor is an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments.
to regulate
to modulate
to regulate is to control or maintain the rate or speed of an object or process.
file
A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding.
to provide
to provide is the capability to make available some object to another that requires it.
nurse
A nurse is an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations.
study subject
A study subject is an individual that is the subject of the study.
x cartesian coordinate
An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system.
y cartesian coordinate
An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system.
z cartesian coordinate
A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system.
study group
A study group is a group of individuals that are subjects in an observational or intervention study.
professor
A professor is an individual that is a scholarly teacher.
student
A student is an individual who is attends an educational institution.
academic
An academic is an individual that participates in education and scholarship.
to increase the rate of formation
to increase the rate of formation is to regulate the rate of formation in a manner that increases this rate relative to a reference process.
to investigate
to investigate is the capability to uncover facts.
mutual disposition
A mutual disposition is a disposition that simulataneously invokes another disposition when realized.
anger
anger is disgust directed toward an equal status individual.
hate
Hate is a deep and emotional extreme dislike, directed against a certain object or class of objects.
love
love is an emotion of a strong affection and personal attachment.
geolegal region
A geolegal region is a geographic region which has causal powers confered by a legal entity.
The 50 kph zones in Ottawa; the geographic region occupied by France.
geographic region
A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth).
The spatial region occupied by the province of ontario; the spatial region occupied by a lake.
geopolitical region
The geographic region bounded by Canada; the spatial region occupied by the US embassy in Ottawa.
a geopolitical region is a geographic region recognized by social or legal convention.
time interval
A time internval is a contiguous temporal region having some duration.
time instant
A time instant is a temporal region which occurs instantaneously, e.g. having no duration.
at this moment; the moment at which a finger is detached in an industrial accident; the moment at which a child is born; the moment of death
table
A table is a figure that consists of an ordered arrangement of columns and rows.
scatterplot
A scatterplot is a statistical graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scatter chart
scatter diagram
scatter graph
year
A year is a period of time taken by a planet to make one revolution around the sun.
month
A month is a period of time that divides the year.
day
A day is a period of 24 hours.
century
A century is a period of one hundred years.
millenium
A millenium is a period of 1000 years
hour
An hour is a period of 60 minutes.
minute
A minute is a period of 60 seconds.
second
A second (symbol: s) is the base unit of time in the International System of Units (SI) and is the second division of the hour by sixty, the first division by 60 being the minute.
informational quality
An informational quality is a quality that pertains to information.
2D cartesian point
A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates.
altitude
Altitude is a distance above sea level.
center of mass
The center of mass (aka barycenter) is the weighted average location of all the mass in a body or group of bodies.
3D cartesian point
A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates.
1D cartesian point
A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates.
line graph
A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments.
Graph 1 in http://tinyurl.com/opwnvm
line chart
bar graph
A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent.
Graphs 3,4,5 in http://tinyurl.com/opwnvm
horizontal bar graph
A horizontal bar graph is a bar graph in which the rectangular bars are horizontally oriented in space.
Graph 3 in http://tinyurl.com/opwnvm
vertical bar graph
A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space.
Graph 4,5 in http://tinyurl.com/opwnvm
stacked bar graph
A stacked bar graph is a bar graph in which each rectangular bar is partioned by the categorical value of each series of data.
Graphs 6,7 in http://tinyurl.com/opwnvm
line-bar graph
A line-bar graph statistical graph that contains both lines and bars.
Graph 8 in http://tinyurl.com/opwnvm
figure part
A figure part is a part of a figure.
plot
A plot is a part of a figure that corresponds to the spatial region between the set of axes.
The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm
axis
An axis is a line segment that is part of a statistical graph in which the position along the line corresponds to a numeric or categorical value.
The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm
The value of a plotted geometric objects (e.g. point) can be obtained from the perpendicular projection of the position of the object onto the axis. Axis may also be associated with a textual description of what the values on the axis represents.
Cartesian coordinate axis
A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system.
x-axis
An x-axis is a Cartesian coordinate axis that is aligned with the horizon.
In most figures, this axis represents categories, such as months, market segments, or other non-numeric data.
The horizontal axis in http://tinyurl.com/opwnvm
y-axis
A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis.
z-axis
A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes.
category axis
A category axis is an axis in which the position along the line is partioned into categories.
The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm
primary category axis
A primary category axis is a category axis that either defines the sole value range or holds the larger set of categorical values specified by the secondary category axis.
The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm
secondary category axis
A secondary category axis is a category axis that defines a finer granular part (or subset) of the value range of the primary category axis.
The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm
value axis
A value axis holds the properties of having a minimum and a maximum value, and is usually associated with tickmarks that indicate intervals along the axis.
A value axis is an axis in which the position along the line is partioned into numeric values.
The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm
left value axis
A left value axis is a value axis that is spatially positioned to the left of the plot area.
right value axis
A right value axis is a value axis that is spatially positioned to the right of the plot area.
scaled value axis
A scaled value axis is a value axis in which the value range was subject to a mathematic transformation.
linear value axis
A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range.
logarithmic value axis
A logarithmic value axis is a scaled value axis that corresponds to a scaling factor of the logarithm of the value range.
data series
A data series is a data set composed of related values displayed in a statistical graph.
Example: The two series that correspond to "Seasonally adjusted" and "Trend" are composed of the seasonally adjusted value of permits in each month and values from a trend derived from some mathematical tranformation across those values, respectively, in Graph 1 of http://tinyurl.com/opwnvm
data point
A data point is a point that which corresponds to the projection of the values of measurement data against the axes of a statistical graph.
global maximal stationary point
A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints.
global minimal stationary point
A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints.
legend
A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities.
The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm
graph title
A graph title is a title that describes a graph.
Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm
primary title
A primary title is a title that should be first used in describing some entity.
secondary title
A secondary title is a title of lesser importance that should be used after the first title in describing some entity.
scientific data
scientific data is data obtained from some scientific procedure.
primary graph title
"Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm
A primary graph title is a primary title that describes a statistical graph.
secondary graph title
A secondary graph title is a secondary title that describes a statistical graph.
biological quality
A biological quality is a quality held by a biological entity.
cellular quality
cellular quality is the quality of a cell
sequence variant role
A sequence variant role is a comparative role in which the composition of characters in a sequence differs when compared to another entity of similar type.
variant role
A variant role is a comparative role in which the value of an attribute differs when compared to another entity
insertion variant role
An insertion variant role is the role of an sequence that contains a sub-sequence that is considered to be an addition relative to the frame of reference.
deletion variant role
A deletion variant role is the role of an sequence that lacks a sub-sequence relative to the frame of reference.
phrase
A phrase is a group of words functioning as a single unit in the syntax of a sentence.
human
A human is a primates of the family Hominidae and are characterized by having a large brain relative to body size, with a well developed neocortex, prefrontal cortex and temporal lobes, making them capable of abstract reasoning, language, introspection, problem solving and culture through social learning.
mouse
A mouse is a small mammal belonging to the order of rodents, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail.
rat
A rat is a medium-sized, long-tailed rodent of the superfamily Muroidea.
worm
A worm is a non-arthropod invertebrate animal that typically have a long cylindrical tube-like body and no legs.
e.coli
Escherichia coli (e coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms.
to consume
to consume is the capability to internalize a material entity.
clause
A clause consists of a subject and a predicate.
to actively interact with
to actively interact with is the capability to interact with another entity in a way that requires physical contact.
person
A person is a being that has certain capacities or attributes constituting personhood.
to decrease the rate of formation
to decrease the rate of formation is to regulate the rate of formation in a manner that decreases this rate relative to a reference process.
polygon vertex
A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon.
polygon edge
A polygon edge is a line segment joining two polygon vertices.
polyhedral skeleton
A polyhedral skeleton is a collection of polygon edges.
polygonal face
A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary.
polyhedral surface
A polyhedral surface is composed of polygonal faces.
polygon
A polygon is a planar entity that is bounded by a closed path or circuit, composed of a finite connected sequence3 of straight line segments.
geometric entity
A geometric entity is an information content entity that pertains to the structure and topology of a space.
point
A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system.
endpoint
An endpoint is a terminal point that is the last of an ordered pair of points.
start point
A start point is a terminal point which is the first of an ordered pair of points.
model
A model is a representation of some thing.
line
A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points.
line segment
A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points.
tick mark
A tick mark is a line segment that is spatially positioned perpendicular to the axis of a statistical graph and indicates the position of a specific numeric value (which may be indicated by an adjacent value label) on a value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value (which may be indicated by an adjacent category label) on the categorical axis.
major tick mark
A major tick mark is a tick mark that indicates the position of a specific numeric value and is adjacent to its value label on the value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value indicated by an adjacent category label on the categorical axis.
minor tick mark
A minor tick mark is a tick mark that indicates the position of a specific numeric value but has no adjacent value label, or is one of a pair of tick marks that delineates the boundary of a categorical value but has no adjacent category label on the categorical axis.
ray
A ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension.
quadrilateral
A quadrilateral is a polygon with composed of four points and four line segments, in which each point is fully connected to two other points.
rectangle
A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair.
bar
A bar is a rectangle that is located in the plot of a statistical graph in which its length is proportional to the values that it represents.
triangle
A triangle is a polygon composed of three points and three line segments, in which each point is fully connected to another point along through the line segment.
directed line segment
A directed line segment is a line segment that is contained by an ordered pair of endpoints (a start point and an endpoint).
arrowed line segment
An arrowed line is a directed line segment in which one or both endpoints is tangentially part of a triangle that bisects the line.
single arrowed line segment
A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line.
double arrowed line segment
A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line.
horizontal line
A horizontal line is a line that is positionally oriented with the horizon.
vertical line
A vertical line is a line that is positionally oriented perpendicular to the horizon.
trend line
A trend line is a line, line segment or ray that is part of a statistical graph which indicates a statistical or visual direction across categorical or value data.
increasing line
An increasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is positive.
decreasing line
An decreasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is negative.
plateau line
An plateau line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is zero.
drop line
A drop line is a statistical graph line that vertically or horizontally connects a data series line with a value axis in a statistical graph.
terminal point
A terminal point is a point that defines the finite extension of a line.
surface normal
A surface normal is a vector that is perpendicular to a flat surface.
positionally oriented line
A positionally oriented line is a line that is positioned against some axis of reference.
statistical graph line
A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data.
to regulate the rate of formation
to regulate the rate of formation is to modify the rate at which an object is formed.
curvature
curvature is a quality of a bearer that relates to the presence of curves, bends, or angles.
straight
straight is a quality of a bearer that is free of curves, bends, or angles.
infinite line
An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points.
vector
A vector is a line which that is bounded by a startpoint and extends outwards along one dimension.
vertex normal
A vertext normal is the normalized average of the surface normals of the faces that contain that vertex.
to serve as
to serve as is the capability to act in a manner corresponding to some role.
to serve as a host
to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself.
to infect
to infect is the capability to administer a disease-causing organism into some object.
polyline
A polyline is a connected sequence of line segments.
polygonal chain, polygonal curve, polygonal path, piecewise linear curve
collection of points
A collection of points is a geometric entity that contains a non-zero set of geometric points.
to cause disease
to cause disease is the capability to materially change a biological object in that it functions abnormally.
to reduce the activation energy
to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond.
to increase the activation energy
to increase the activation energy is to require a larger amount of energy in order to form or break a chemical bond.
to change the activation energy
to change the activation energy is to change the amount of energy required to form or break a chemical bond.
normal
A quality that has a value that is normal or average.
abnormal
A quality that has a value that is outside normal or average.
lipid residue
A lipid residue is a part of an organic molecule that was derived from a lipid molecule.
chemical synthesis
chemical synthesis is synthesis of a chemical entity from physical precursors through one or more chemical interactions or reactions.
molecular orbitral
A molecular orbital (or MO) is a mathematical function describing the wave-like behavior of an electron in a molecule.
passive transport
passive transport is the movement of a substance across a membrane and does not require chemical energy.
diffusion
diffusion is motion of particles at temperatures above absolute zero.
diffusion equation
A diffusion equation describes density fluctuations in a material undergoing diffusion.
movement equation
A movement equation describes the displacement of an object in space over time.
ordinary differential equation
An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable.
partial differential equation
A partial differential equation (PDE) is a differential equation in which the unknown function is a function of multiple independent variables and the equation involves its partial derivatives.
differential equation
A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders.
movement
movement is the process in which an object is spatially displaced.
brownian motion
Brownian motion is the seemlingly random movement of particles suspended in a fluid.
osmosis
osmosis is the movement of water molecules through a selectively-permeable membrane down a water potential gradient.
passive movement
passive movement is the process in which an object is spatially displaced without an expenditure of energy contained in molecular bonds.
active movement
active movement is the process in which an object is spatially displaced using some chemical energy.
transporting
transporting is a process in which one object physically moves another object from one location to another.
membrane transport
membrane transport is the movement of molecules across a membrane.
primary active transport
primary active transport, also called direct active transport, directly uses energy to transport molecules across a membrane.
secondary active transport
secondary active transport or co-transport uses electrochemical potential difference created by pumping ions out of the cell to transport molecules across a membrane.
symport enabled secondary active transport
symport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in the same direction simultaneously.
antiport enabled secondary active transport
antiport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in opposite directions simultaneously.
locomotion
The self-propelled movement of an object.
birthing
brirthing is the process by which a biological organism is brought into existence.
dying
dying is a process in which a biological entity ceases to exist.
idea
An idea is a proposition about some object of conceptual thought.
biological reproduction
biological reproduction is the biological process by which one or more biological organisms are produced from their "parents".
creating
creating is the process in which an entity comes into existence.
regulating
regulating is a process that modulates the attributes of an object or process.
regulation
biosynthesis
biosynthesis is the synthesis of an organic compound in a living organism, usually aided by enzymes.
destroying
destroying is a process in which something is broken down and/or ceases to exist.
destruction
chemical destruction
chemical destruction is destruction of a chemical entity to its chemical constituents through one ormore chemical interactions or reactions.
interacting
interacting is a process characterized by the interaction between two or more entities.
data transformation
data transformation is the process of applying an algorithmic procedure to some input data and producing some output data.
parameterized data transformation
A parameterized data transformation is a data transformation whose behaviour may be modified by one or more parameters.
data storage device
A data storage device is a device that is capable of storing information.
solid state hard drive
A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data.
hard disk drive
A hard disk drive (HDD) is a non-volatile, random access device for digital data. It features rotating rigid platters on a motor-driven spindle within a protective enclosure. Data is magnetically read and written on the platter by read/write heads that float on a film of air above the platters.
structure
structure is the specification that refers to the composition and arrangement of parts of an object.
computational entity
A computational entity is an information content entity operated on using some computational system.
sound wave
A sound wave is a mechanical wave that is an oscillation of pressure transmitted through a solid, liquid, or gas, composed of frequencies within the range of hearing.
curve
A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself.
regulation of process
regulation of a process is a process that modulates the duration, frequency, spatial extent of a target process.
regulation of capability
regulation of capability is the regulation of the ability of one party by another.
regulation of catalytic capability
the regulation of the enzymatic activity.
representation
A representation is a entity that in some way represents another entity (or attribute thereof).
ordinal position
A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities.
attribute
An attribute is a characteristic of some entity.
collection
A collection is a set for which there exists at least one member, although any member need not to exist at any point in the collection's existence.
empty set
An empty set is a set for which there are exactly 0 members.
standard
A standard is a socially-agreed upon specification.
regulatory authority
A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity.
collective
A collective is a group of entities that share or are motivated by at least one common issue or interest, or work together on a specific project(s) to achieve a common objective.
formal specification
A formal specification is a mathematical description of software or hardware that may be used to develop an implementation.
RDFS ontology
An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS).
OBO ontology
An OBO ontology is an ontology document as specified by the Open Biological Ontology community.
chemical functional group
A chemical functional group is a covalently connected part of a molecule which normally confer specific chemical properties.
chemical structure
chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure.
molecular structure
molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together.
probability measure
A probability measure is quantity of how likely it is that some event will occur.
to passively interact with
to passively interact with is the capability to interact with another entity in a way that does not require physical contact.
increased
A quality that has a value that is increased compared to normal or average.
process model
A process model is a representation of some process.
object model
An object model is a representation of an object.
information processing
information processing is a process that involves the generation or use of information.
wave
A wave is a physical entity that travels through space and time, consist of oscillations or vibrations and may be accompanied by the transfer of energy.
textual entity
A textual entity is language entity that is manifested as one or more distinct characters.
version label
A version label is a label for a particular form or variation of an earlier or original type.
software version label
A software version label is a version label for a piece of software.
major.minor[.build[.revision]]
hole
A hole is a site that is opening into or through something.
province
A province is a territorial unit, almost always an administrative division, within a country or state.
state
A state is a set of governing and supportive institutions that have sovereignty over a definite territory and population.
territory
A territory is a non-sovereign geographic region.
country
A country is a region legally identified as a distinct entity in political geography.
city
A city is a relatively large and permanent settlement.
township
A township is a rural or sub-urban settlement.
sofware execution
software execution is the process of executing software on a computing device.
start time
A start time is a time instant pertaining to the time at which a process begins.
end time
An end time is a time instant pertaining to the time at which a process ends.
unique identifier
A unique identifier is an identifier that uniquely identifies some thing.
social role
A social role is a role that is ascribed to individuals in a community.
processual role
A processual role is a role that can only be realized in a process.
abstract role
An abstract role is a role whose basis lies in spatial/temporal or comparative relations.
justification
A justification is a proposition that defends, explains or excuses some argument.
academic department
An academic department is a division of a university or school faculty devoted to a particular academic discipline.
institute
institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective.
to be a part of
to be a part of is the capability to be assembled into a larger structure that persists in time.
to associate
to associate is the capability to physically interact with another object.
to be actively interacted with
to be actively interacted with is the capability to be manipulated by some device or agent.
corporation
A corporation is an organization that is granted a charter recognizing it as a separate legal entity.
to be passively interacted with
to be passively interacted with is the capability of an object to be observed.
to be recorded
to be recorded is the capability of an object to be observed in such a way that information about it can be transcribed in a specified format on some physical medium.
to be observed
to be observed is the capability of an object to be perceived.
to disassemble
to disassemble is to physically separate the parts of an object.
to disassociate
to disassociate is to cease or break association with some thing.
to interact with
to interact with is a capabililty that involves another object.
to be interacted with
to be interacted with is the capability of an object to be target of a physical interaction.
evolving
evolving is a process that elicits change across successive generations in the inherited characteristics of biological populations.
positional role
A positional role is an abstract role which holds by comparing position to another object of reference.
design
A specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints.
occupational role
An occupational role is a social role that pertains to an organizational structure.
student role
A student role is the role of an individual that is enrolled in courses at an academic institution.
professor role
A professor role is the role of an individual that is involved in teaching of students (undergraduate and/or graduate) at a post-secondary academic institution.
academic role
An academic role is a social role that pertains to the academic institution.
medical role
A medical role is the role of an individual that is a participant in the delivery of medical care.
doctor role
A doctor role is the role of an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments.
physician
nurse role
A nurse role is the role of an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations.
patient role
A patient role is the role of an individual that is the recepient of medical care.
medical practitioner
A medical practioner is an individual that provides medical care.
dentist role
A dentist role is the role of an individual that that specializes in the diagnosis, prevention, and treatment of diseases and conditions of the oral cavity.
to translocate
to move
to translocate is the capability to displace oneself from one location to another.
to be translocated
to be moved
to be translocated is the capability to be physically displaced from one location to another
comparative role
A comparative role is an abstract role which holds by comparing some attribute of another object of reference.
to be compared
to be compared is the capability of an object to be examined in order to note the similarities or differences among a set of objects.
to compare
to compare is the capability to examine in order to note the similarities or differences among a set of objects.
to examine
to examine is the capability to make detailed observation.
to be examined
to be examined is the capability of an object to be observed in a detailed manner.
administrative role
An administrative role is the role of an individual that performs administrative tasks for some organization.
secretary role
A secretary role is the role of an individual that performs administrative tasks to support one or more individuals of the same organization.
chemical identifier
A chemical identifier is an identifier for a chemical entity
record identifier
A record identifier is an identifier for a database entry.
physical entity identifier
A physical entity identifier is an identifier for a physical entity.
informational entity identifier
An informational entity identifier is an identifier for an informational entity.
molecular identifier
A molecular identifier is an identifier for a molecular entity.
planning
planning is the agentive process of developing a plan that specifies a set of actions in order to meet a set of goals or objectives.
curve segment
A curve segment is a part of a curve that consists of at least three points.
stationary point
A stationary point is a point that is part of a curve in which the derivative at that point is zero, and hence its value is at least a local maximum or minimum.
local maximum stationary point
A local maximum stationary point is a point that has a higher value in some axis than adjacent points.
local minimum stationary point
A local minimum stationary point is a point that has a lower value in some axis than adjacent points.
learning
learning is the agentive process of acquiring knowledge.
comparing
comparing is the process of examining a set of objects and determining their equality or inequality based on one or more features.
reasoning
reasoning is the agentive process of using knowledge to evaluate the truth value of a proposition.
investigation
investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study.
predicting
predicting is the process of formulating a proposition about a state of affairs which might be realized in the future.
database
A database is a set of tables.
decreased
A quality that has a value that is decreased compared to normal or average.
row
A row represents a single, implicitly structured data item in a table.
column
A column is a vertical sequence of cells in a cellular automata.
database table
A database table is a set of named columns with zero or more rows composed of cells that contain column values and is part of a database.
cell (informational)
The minimal unit of a cellular automaton that can change state and has an associated behavior.
database entry
A database entry is a single, implicitly structured data item in a table.
database column
A database collumn is a column in a database table.
disordered
disordered is a structural quality in which the parts of an object are non-rigid.
unique cell
A unique cell is a cell that contains a unique value in the cellular automaton.
referencing cell
A referenceing cell is a cell of a cellular automata that refers to another cell.
referent cell
A referent cell is a cell that is the referent of some function or pointer.
database key
A database key is an informational entity whose value is constructed from one or more database columns.
primary database key
A primary database key is a database key that identifies every row of a table.
foreign database key
A foreign database key is a database key that refers to a key in some table.
probability value
A p-value or probability value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true
p-value
street name
A street name is the token given to identify a particular street.
postal code
A postal code is a geographic coordinate composed of a series of letters and/or digits appended to a postal address for the purpose of sorting mail.
apartment number
An apartment number is the number assigned to identify an apartment in a building of apartments.
uncertainty value
The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value.
standard deviation
A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value).
versioned record
A versioned record is a record for which there exists another variant based that was derived via modification of the facts.
object
An object is an entity that is wholly identifiable at any instant of time during which it exists.
to be a member of
to be a member of is the capability to be considered a part of a collection.
to distort
to distort is the capability to change the appearance of an entity by some transformation.
primer
A primer is a nucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.
to bind to
to bind to is the capability to physically interact with another object through a set of non-covalent interactions.
spatial boundary
A spatial boundary is the closure minus the interior of a subset of a topological space.
hermaphrodite
hermaphrodite is a biological sex of an individual with both male and female sexual organs.
answer
An answer is a reply to a question.
verbal language entity
A verbal language entity is a language entity that is manifested through sound.
page number
A page number is the count of a page in a sequence of pages.
linear position
A linear position is the position of some object against a linear positioning system.
sequence element position
A sequence element position is the position of an element of a linear sequence.
non-protein coding RNA (ncRNA) gene
A non-protein coding RNA (ncRNA) gene is a gene that encodes for a RNA transcript that is not further translated into a protein product.
ncRNA gene
sequence start position
A sequence start position is the start position for a sequence of characters.
sequence end position
A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference.
count
The number of elements of a finite set of objects.
chemical entity role
A chemical role is a processual role held by a chemical entity.
catalytic role
The role of a chemical participant that serves to increase the rate of reaction by lowering the activiation energy.
substrate role
The role of a chemical entity that is modified in a chemical reaction.
product role
The role of a chemical entity present at the end of a chemical reaction.
cofactor role
The role of a chemical entity involved in the mechanism for enzyme-mediated catalysis.
co-enzyme role
A co-factor role in which the chemical entity is modified during catalysis and must be regenerated.
prosthetic group role
A coenzyme role of a chemical entity that is covalently bonded to the enzyme.
co-substrate role
A co-enzyme role of a chemical entity that is transiently associated, and is regenerated in a separate reaction.
inhibitor role
The role of a chemical entity that reduces the rate of reaction.
activator role
The role of a chemical entity that increases the rate of reaction.
charged
The quality of having a charge.
uncharged
The quality of not having a charge.
partial positive charge
A partial negative charge is a negative charge where the value of the charge is negative.
partial negative charge
A partial positive charge is a partial charge where the value of the charge is positive.
partial charge
The quality of having a charge that is not a full multiple of 1 unit charge.
complete charge
A complete charge is a charge where the value of the charge is a multiple of 1.
URL
A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource.
Uniform Resource Locator
affection
affection is an emotion characterized with a feeling or type of love for another living thing.
angst
angst is the intense feeling of apprehension, anxiety or inner turmoil.
annoyance
Annoyance is an unpleasant emtion that is characterized by a abnormal or excessive sensitivity to some external stimulus.
anxiety
anxiety is an emotion charactersized by intense feeling of fear and concern coupled with a physical response.
apathy
apathy is an emotion characterized by lack of interest, enthusiasm, or concern.
arousal
arousal is an emotion characterized by state of reactive to stimuli. It involves the activation of the reticular activating system in the brain stem, the autonomic nervous system and the endocrine system, leading to increased heart rate and blood pressure and a condition of sensory alertness, mobility and readiness to respond.
awe
awe is an emotion produced by that which is grand, sublime or powerful and is characterized by a combination of joy, fear and admiration/reverence/respect.
boldness
boldness is the trait of being willing to undertake things that involve risk or danger.
boredom
boredom is the emotion experience by those not interested in their surroundings or available activities.
contempt
contempt is disgust towards a lower status individual.
contentment
contentment is an emotion characterized by acknowledgement and satisfaction of the current state of affairs.
curiosity
curiosity is the strong desire to know or learn something.
depression
depression is an unpleasant emotion linked to aversion to activity that can affect a person's thoughts, behavior, feelings and physical well-being. Depressed individuals may feel sad, anxious, empty, hopeless, worried, helpless, worthless, guilty, irritable, or restless.
desire
desire is a strong emotion of wanting to have something or wishing for something to happen.
despair
despair is depression, hopelessness or lack of hope.
disappointment
disappointment is the feeling of dissatisfaction that follows the failure of expectations or hopes to manifest.
disgust
Disgust is a feeling of revulsion or profound disapproval aroused by something unpleasant or offensive.
dread
dread is the instense negative emotion that induces fear and apprehension.
ecstasy
ecstacy is an emotion characterized by a heightened state of consciousness with total involvement of a subject.
positive emotion
A positive emotion is an emotion that feels good.
negative emotion
negative emotion is an emotion that does not feel good.
embarassment
Embarrassment is the emotion of intense discomfort with oneself, experienced upon having a socially unacceptable act or condition witnessed by or revealed to other.
envy
envy is an emotion that occurs when a person lacks another's (perceived) superior quality, achievement or possession and wishes that the other lacked it.
euphoria
euphoria is an emotion characterized by intense feelings of well-being, elation, happiness, ecstasy, excitement, and joy.
excitement
excitement is a positive emotion of feeling great enthusiasm and eagerness.
fear
Fear is a negative emotion induced by a perceived threat that induces one to hide or move quickly away from the location of the perceived threat.
frustration
Frustration is an emotion that arises from the perceived resistance to the fulfillment of individual will.
gratitude
Gratitude, thankfulness, gratefulness, or appreciation is a feeling, emotion or attitude in acknowledgment of a benefit that one has received or will receive.
happiness
happiness is an emotion characterized by positive or pleasant emotions ranging from contentment to intense joy.
guilt
Guilt is the emotion borne from feeling responsible for the commission of an offense and arises out of public humiliation.
grief
grief is an emotion in response to loss, whether physical or abstract including death, unemployment, ill health or the end of a relationship.
hope
hope is an emotion of belief in a positive outcome related to events and circumstances in one's life.
hostility
Hostility is the intense negative emotion of being in conflict or opposition to someone or something.
hurt
hurt is an unpleasant feeling, emotion or sensation.
hysteria
Hysteria is an unmanageable emotion.
indifference
indifference is an emotion characterized by lack of interest, concern, or sympathy.
interest
interest is the emotion of wanting to know or learn about something or someone.
jealousy
jealousy is an emotion and typically refers to the negative thoughts and feelings of insecurity, fear, and anxiety over an anticipated loss of something that the person values, particularly in reference to a human connection.
joy
joy is an emotion of intense happiness.
loathing
loathing is an intense dislike or disgust.
loneliness
Loneliness is an unpleasant emotion in which a person feels a strong sense of emptiness, yearning distress and solitude resulting from inadequate quantity or quality of social relationships.
lust
lust is the strong desire for sex.
misery
misery is a feeling of great unhappiness, suffering and/or pain.
panic
Panic is a sudden emotion of fear which is so strong as to dominate or prevent reason and logical thinking, replacing it with overwhelming feelings of anxiety and frantic agitation consistent with an animalistic fight-or-flight reaction.
passion
passion is the intense desire for something.
pity
Pity is the emotion of sadness or sorrow for another.
pleasure
pleasure is an emotion of happy satisfaction and enjoyment.
pride
pride is an emotion of satisfaction of attachment toward one's own or another's choices and actions, or toward a whole group of people, and is a product of praise, independent self-reflection, or a fulfilled feeling of belonging.
rage
Rage is a feeling of intense anger that is associated with the Fight-or-flight response.
regret
regret is a feeling of sadness, repentance, or disappointment over something that has happened or been done.
remorse
remorse is an emotion of personal regret felt by a person after he or she has committed an act which they deem to be shameful, hurtful, or violent.
sadness
sadness is emotional pain associated with, or characterized by feelings of disadvantage, loss, despair, helplessness, sorrow, and rage.
satisfaction
satisfaction is an emotion of fulfillment of one's wishes, expectations, or needs, or the pleasure derived from this.
shame
shame is the emotion borne from feeling responsible for the commission of an offense.
shock
shock is an emotion of sudden upset or surprise.
shyness
shyness is an emotion of apprehension, lack of comfort, or awkwardness experienced when in proximity to, approaching, or being approached by other individuals, especially in new situations or with unfamiliar individuals.
sorrow
sorrow is the emotion that is characterized by a long term state of intense sadness, distress and a degree of resignation (not accepting).
suffering
Suffering is the unpleasant emotion and aversion associated with the perception of harm or threat of harm in an individual.
surprise
surprise is a brief emotion experienced as the result of an unexpected event.
terror
terror is the extreme feeling of fear.
wonder
wonder is an emotion of perceiving something very rare or unexpected, but not threatening.
worry
worry is the emotion characterized by concer over a real or imaginary issue.
department chair role
A department chain role is the role of an individual that heads a department at a academic organization.
student advisor role
A student advisor role is the role of an individual employed at an academic organization that is involved in advising students.
undergraduate student advisor role
An undergraduate student advisor role is the role of an individual employed at an academic organization that is involved in advising undergraduate students.
graduate student advisor role
A graduate student advisor role is the role of an individual employed at an academic organization that is involved in advising graduate students.
reactant role
The role of a chemical entity present at the beginning of a chemical reaction.
regulator role
The role of a chemical entity that modifies the rate of reaction.
investigational role
An investigational role is a role held by participants involved in an investigation.
host role
The role of an organism in providing resources to maintain the survival and/or reproduction of another organism.
subject role
A subject role is the role of an individual that is the target of the study.
publishing role
A publishing role is the role of an individual that is involved in the preparation and issue of creative works for consumption by a wider audience.
publisher role
A publisher role is the role of an individual that prepares and issues creative works.
author role
An author role is the role of an individual that creates a creative, written work.
buffer role
A buffer role is the role of a chemical substance which maintains a pH at a near constant value.
chemical substance role
A chemical substance role is a chemical entity role held by a chemical substance.
molecular entity role
A molecular entity role is a chemical entity role held by a molecule.
toxin role
A toxin role is a toxic role of a chemical substance that is poisonous and is produced by an organism.
toxic role
A toxic role is the role of a chemical substance that is poisonous.
reagent role
A role of a chemical substance that participates in a chemical reaction as part of some scientific investigation.
to luminesce
to luminesce is to emit light through cold body radiation
to fluoresce
to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation.
molecular tracer role
A molecular tracer role is a reactant role of a molecular entity that serves as a marker for the presence, abundance, or location of a molecular target that it associates with.
association
An assocation is a relationship between two or more entities derived by some informational analysis.
statistical association
A statistical association is any relationship between two measured quantities that renders them statistically dependent.
chromosome
A chromosome is a molecular complex of circular or linear DNA and bound proteins.
top value axis
A top value axis is a value axis that is spatially positioned to the top of the plot area.
bottom value axis
A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area.
chart
A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures.
map
A map is a a visual representation of an area that depicts the relationship between elements of that space.
heatmap
A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors.
steamgraph
A steamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis.
boxplot
A boxplot (box-and-whisker diagram) is a convenient way of graphically depicting groups of numerical data through their five-number summaries: the smallest observation (sample minimum), lower quartile (Q1), median (Q2), upper quartile (Q3), and largest observation (sample maximum).
geographic heatmap
A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors.
histogram
A histogram is a graphical representation of data which consists of tabular frequencies, shown as adjacent rectangles, over discrete intervals (bins) , with an area equal to the frequency of the observations in the interval.
measurement scale
A measurement scale is a functional specification that specifies an allowed range of categories or values.
nomimal scale
A nominal scale of measurement only specifies a limited set of categories.
binary scale
A binary scale is a measurement scale that specifies a choice between two values.
numeric scale
A numeric scale of measurement is one that only specifies numeric values.
decimal scale
A decimal scale of measurement is one that only specifies decimal values.
integer scale
An integer scale of measurement is one that only specifies integer values.
modifying
modification
modifying is the process by which an entity gains or loses parts, qualities, roles, dispositions, functions, etc, but maintains their identity through these changes.
reproducing
reproducing is a process characterized by creation of an entity that is similar or exactly the same as the template from which it is derived.
independent variable
An independent variable is a variable that may take on different values independent of other elements in a system.
dependent variable
A dependent variable is one whose value changes as a consequence of changes in other values in the system.
Gantt chart
A Gantt chart is a bar chart that illustrates a project schedule.
correlation
A correlation is a statistical relationship involving dependence between two random variables or datasets.
television program
A television program is a audiovisual media that is produced and broadcast using a television.
radio receiver
A radio receiver is a communication device that receives its input from an antenna, uses electronic filters to separate a wanted radio signal from all other signals picked up by this antenna, amplifies it to a level suitable for further processing, and finally converts through demodulation and decoding the signal into a form usable for the consumer, such as sound, pictures, digital data, measurement values, navigational positions.
telephone
The telephone is a communications device that transmits and receives sounds, and are minimally composed of a microphone to speak into, a speaker'which reproduces the voice of the other person and a ringer which makes a sound to alert the owner when a call is coming in.
radar
A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects.
pie chart
A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents.
matrix chart
A matrix chart summarizes a multidimensional data set in a grid.
network diagram
A network diagram consists of a set of vertices connected by edges.
block histogram
A block histogram contains an x-axis that is divided into bins which correspond to value ranges. Each item in the data set is drawn as a rectangular block, and the blocks are piled into the bins to show how many values in each range.
bubble chart
A bubble chart contains circles whose area corresponds to a value.
stack graph
A stack graph is a statistical graph which presents multiple series in which the distance between one series and another indicates the relative contribution to the total for any x-value.
treemap
A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value.
word tree
A word tree is a chart that links phrases with contexts through a tree-like branching structure.
textual chart
A textual chart is a chart containing text.
tag cloud
A tag cloud is a visualization of word frequencies.
word cloud
phrase net diagram
A phrase net diagram illustrates the relationship between different words used in a text.
mereological chart
A mereological chart is a chart that illustrates the parts in the context of the whole.
conversing
conversing a form of interactive, spontaneous communication between two or more agents who are following rules of etiquette.
numeric label
A numeric label is a number used as a label.
start position
A start position is the proximal position of an object relative to an origin in a linear system.
interval
An interval is a set of real numbers that includes all numbers between any two numbers in the set.
tree diagram
A tree diagram is a hierarchical network diagram in which a root vertex is connected to one or more other vertices through a directed edge, which in turn may be connected to other vertices.
flowchart
A flowchart is a diagram that represents an algorithm or process, showing the steps as boxes of various kinds, and their order by connecting these with arrows.
venn diagram
A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles.
dendrogram
A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering.
apprehension
apprehension is the negative emotion that something unpleasant will occur.
resentment
resentment is disgust directed toward a higher status individual.
pain
Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
default parameter
A default parameter is a parameter which has a default value.
end position
An end position is the distal position of an object relative to an origin in a linear system.
sick
sick is the status of a living organism that is behaving at a sub-optimal level.
environment
An environment is a geographic region that hosts certain processes or objects.
device
A device is usually a constructed tool.
communication device
A communication device is a device that facilitates the transmission of information through encoded in an audio or digital signal between a sender and a receiver.
existence quality
existence quality is the quality of an entity that describe in what environment it is known to exist.
real
real is the quality of an entity that exists in real space and time.
fictional
fictional is the quality of an entity that exists only in a creative work of fiction.
virtual
virtual is the quality of an entity that exists only in a virtual setting such as a simulation or game environment.
not started
not started is the status of a process that is predicted to exist but has not yet begun.
standard operating procedure
A standard operating procedure is a specification approved for use in specific environments.
agreement quality
agreement quality is a quality that exhibits the degree of consensus for some set of assertions.
agreement
agreement is the result of consensus decision making when members of the group agree.
disagreement
agreement is the result of consensus decision making when members of the group do not all agree.
poison role
A poison role is the role of a substance that causes some negative disturbance in an organism.
communicating
communicating is the process of conveying information through the exchange of thoughts, messages, or information, as by speech, visuals, signals, writing, or behaviour.
observational study
observational study draws inferences about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator
syllable
A syllable is a verbal entity of language having one vowel sound, with or without surrounding consonants, forming the whole or a part of a word.
consonant
A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract.
vowel
A vowel is a verbal entity of language that is pronounced with an open vocal tract so that there is no build-up of air pressure at any point above the glottis.
sign language
A sign language (also signed language) is a language that involves manual communication and body language to convey meaning. This can involve simultaneously combining hand shapes, orientation and movement of the hands, arms or body, and facial expressions to fluidly express a speaker's thoughts.
verbal language
A verbal language is a language that uses sounds to communicate.
written language
written language is a language that is communicated through a writing system.
gene-disease association
A gene-disease association is an association between a gene and a disease.
genome
A genome is a collection of nucleic acids.
protein coding gene
A gene that contains an open reading frame which codes for a protein.
functional rna coding gene
A gene that codes for a functional RNA molecule.
predicted gene
A predicted gene is a gene that was identified through computational method but has not been experimentally validated.
pseudogene
A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated.
sequence assembly
A sequence assembly is a sequence that is produced as by the alignment of two or more sequences.
validated gene
An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods.
unsupported
unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical)
chemical-disease association
A chemical-disease association is an association between a chemical and a disease.
experiment
An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis.
suspended
suspended is the status of a process that is no longer progressing towards completion.
cancelled
cancelled is a process status in which the process, while planned to occur, will not occur.
aborted
aborted is a process status in which a started process will not complete as intended.
literature curation
literature curation is the process of an agent selecting and extracting terms and phrases from a document.
procedure
A procedure is a process that attempts to achieve one or more objectives by following an established set of actions.
clinical trial
A clinical trial is an intervention trial to determine the safety and efficacy of medical interventions (e.g., drugs, diagnostics, devices, therapy protocols).
medical diagnosis
A medical diagnosis (often simply termed diagnosis) refers to the process of attempting to determine or identify a possible disease or disorder.
differential diagnosis
A differential diagnosis (sometimes abbreviated DDx, ddx, DD, D/Dx, or ΔΔ) is a systematic diagnostic method used to identify the presence of an entity where multiple alternatives are possible (and the process may be termed differential diagnostic procedure), and may also refer to any of the included candidate alternatives (which may also be termed candidate condition).
diagnostic opinion
A diagnostic opinion is an opinion resulting from a medical diagnostic procedure.
opinion
An opinion is a belief that is the result of emotion or interpretation of facts.
drug effect
A drug effect is a chemical interaction in which a chemical elicits a marked characteristic of a biological system.
drug drug interaction
A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response.
assay
An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.
toxicity
toxicity is the quality of a chemical substance to cause injury to an organism in a dose dependent manner.
toxic
toxic is the quality of a substance imparing the normal functioning of a system.
non toxic
non toxic is the quality of a substance having no damaging effect to a system.
chemical quality
chemical quality is the quality of a chemical entity.
healthy
healthy is an organismal state of complete physical, mental and social well-being.
age
age is the length of time that a person has lived or a thing has existed.
ethnicity
ethnicity is the biological quality of membership in a social group based on a common heritage.
race
race is a characteristic of an individual by heritable phenotypic characteristics, geographic ancestry, physical appearance, ethnicity, and social status.
ethnic group
An ethnic group is a group of people whose members identify with each other through a common heritage, consisting of a common culture, including a shared language or dialect.
syndrome
A syndrome is composed of a set of several clinically recognizable features, signs (observed by someone other than the patient), symptoms (reported by the patient), phenomena or characteristics that often occur together.
ratio
A ratio is a relationship between two numbers of the same kind expressed arithmetically as a dimensionless quotient of the two which explicitly indicates how many times the first number contains the second.
dose
A dose is the quantity of a chemical substance administered to a biological system.
effective dose
effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population.
expected value
An expected value (or e-value) is the weighted average of all possible values that a random variable can take on.
diagnostic test
A diagnostic test is a procedure performed to confirm, or determine the presence of disease in an individual suspected of having the disease, usually following the report of symptoms, or based on the results of other medical tests.
medical screening
A medical screening is a medical test or series used to detect or predict the presence of disease in individuals at risk for disease within a defined group, such as a population, family, or workforce
medical procedure
A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder.
prognosis
A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence.
report
A report is a textual document made that present focused, salient content to a specific audience.
medical health record
A medical health record is a record of a single patient's medical history.
medical report
A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual.
peer reviewed article
A peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication.
major version number
A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version.
minor version number
A minor version number is a version of a software that exhibits minor features or significant fix from a prior version.
revision number
A revision number is a version of a software in which bugs have been fixed from a prior version.
text quality
text quality is the quality of a textual entity.
reviewed
reviewed is the quality of a textual entity that has been examined and commented on by another party.
peer-reviewed
peer-reviewed is the quality of a textual entity that has been examined and commented by a peer expert reviewer.
draft
draft is the quality of text that has not yet complete.
finalized
finalized is the quality of a textual entity that is in its final form.
editor reviewed
editor reviewed is the quality of a textual entity that has been examined and commented on by an editor.
written
written is the quality of information that is embodied as visual glyphs in some material form.
morpheme
A morpheme is the smallest semantically meaningful unit in a language.
study design
A study design is a protocol for the proper execution of a study which normally requires a carefullly crafted research question or hypothesis and at least one variable under observation and observed values for that variable.
recipe
A recipe is a set of instructions that describe how to prepare or make something.
experimental protocol
An experimental protocol is an action specification with respect to the design and implementation of experiments. In addition to providing a detailed set of procedures and lists of required equipment and instruments, experimental protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias.
viroid
A viroid is a molecule of RNA that does not code for and is not protected by a protein coat.
polar quality
The quality of being polar or not polar.
polar
polar is the quality of having a dipole.
non-polar
non-polar is the quality of not having a dipole.
intervention study
An intervention study has the objective of improving the condition of an individual or a group of individuals, and demonstrates the magnitude of that capability by comparing it to a control group.
sampling
sampling is the act of obtaining a sample, whether through selection, collection or preparation.
sample
A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
data analysis
data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making.
data collection
data collection is the process of acquiring information.
reason
A reason is a justification that specifies the motive for an action or a determination.
measuring
measurement
measuring is the process of determining the size, amount, or degree of (something) by using an instrument or device marked in standard units
observing
observation
observing is a process of passive interaction in which one entity makes note of attributes of one or more entities.
character position
The ordinal position of a character in a sequence of characters.
word start position
The position of the first character in a word as an offset from the first character of the text in which it is found.
word end position
word end position is the position of the last character in a word as an offset from the first character of the text in which it is found.
gesturing
gesturing is a form of non-verbal communication in which visible bodily actions communicate particular messages, either in place of speech or together and in parallel with spoken words. Gestures include movement of the hands, face, or other parts of the body.
planned
planned is a process status for a process that has not yet started, but is referred to in a plan.
population
A population is all the organisms that both belong to the same group or species and live in the same geographical area.
human population
A human population refers to a collection of human beings.
family
A group of people affiliated by consanguinity, affinity, or co-residence.
community
A community is a sizeable social unit that shares common values.
speculation
speculation is an opinion based on incomplete evidence.
study
A study is a process that realizes the steps of a study design.
controlled observational cohort study
In a controlled observational cohort study, two groups of subjects are selected from two populations that are thought to differ in only one characteristic. The groups of subjects are studied for a specific period and contrasted at the end of the study period.
control group
A control group is a group of individuals that are not subject to an intervention of interest, but rather serve as a baseline to compare the outcomes in the intervention group.
intervention group
An intervention group is a group of individuals that are subject to an intervention.
control variable
A control variable that is believed to alter the dependent or independent variables, but may not actually be the focus of the experiment. So that variable will be kept constant or monitored to try to minimise its effect on the experiment.
text span start position
text span start position is the position (offset) of the first character of a text span in relation the text it is from.
text span end position
text span end position is the position (offset) of the last character of a text span in relation the text it is from.
text span
A text span is a subset of contiguous sequence of characters of a textual entity.
t-statistic
A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error.
microarray probe set identifier
A microarray probe set identifier is an identifier for a set of probe pairs selected to represent expressed sequences on an array.
microarray experiment
A microarray experiment is an experiment that involves a microarray device to measure the expression of one or more genes.
gene expression value
A gene expression value is a measured value obtained from a gene expression experiment.
differential gene expression ratio
A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample.
genotype
A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof).
vocabulary
A vocabulary is a collection of terms.
t-statistic based increased differential gene expression
A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero.
t-statistic based decreased differential gene expression
A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero.
date of database submission
A date of database submission refers to the moment in time in which some information was submitted/received to a database system.
liquid solution
A liquid solution is a heterogeneous substance in a liquid state.
to remove a covalent bond
to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond.
to add a covalent bond
to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond.
to modify electronically
to modify electronically is the capability to change the electronic properties of an object.
concentration
concentration is the quantity of a constituent divided by the total volume of a mixture.
pH is a measure of the activity of the (solvated) hydrogen ion.
pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution.
homogeneous
homogeneous is a quality that describes the uniform composition of an object.
heterogeneous
homogeneous is a quality that describes the varied composition of an object.
structural quality
A structural quality is a quality of an object that describes its structure.
rigid
rigid is the quality of maintaining structural integrity (and not bending) under pressure.
bent
bent is the quality of a line being sharply curved or having an angle.
curved
curved is the quality of a line that deviates from straightness in a smooth, continuous fashion.
electronic structure
electronic structure is the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals.
the electron configuration of the neon atom is 1s2 2s2 2p6.
crystal structure
A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid.
to interact and to be interacted with
to interact and to be interacted with is a mutual disposition of interacting objects.
to gain a covalent bond
to gain a covalent bond is the capability of a chemical entity to have bonds added.
to lose a covalent bond
to lose a covalent bond is the capability of a chemical entity to have bonds removed.
to ingest
to ingest is the capability to take into the body by the mouth for digestion or absorption.
to produce
to produce is the capability to create new objects
pathway
A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective.
centrality measure
A central tendency measure is a central value or a typical value for a probability distribution.
mean
A mean is the central tendency of a collection of numbers taken as the sum of the numbers divided by the size of the collection.
median
A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half.
mode
A mode is the value that appears most often in a set of data.
sum
A sum is the result of adding a set of values together.
minimal value
A minimal value is smallest value of an attribute for the entities in the defined set.
maximal value
A maximal value is largest value of an attribute for the entities in the defined set.
member count
A count of the instances of a class or members in a collection.
union
A union is a list of all of the values of an attribute for the entities in the defined set.
intersection
An intersection is a list of only the values of an attribute for the entities in the defined set where all entities have that value.
sequence
A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms).
For example, (M, A, R, Y) is a sequence of letters that differs from (A, R, M, Y), as the ordering matters, and (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence.
gene-disease association linked with causal mutation
A gene-variant disease association in which a mutation in the gene/protein results in the development or maintenance of the disease.
therapeutic gene-disease association
A gene disease association in which the gene is a therapeutic marker for the disease.
gene-disease association arising from a therapeutic role of the gene/protein
gene-disease biomarker association
A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease.
gene-disease association linked with genetic variation
A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease.
gene-disease association linked with altered gene expression
A gene-disease association in which the disease phenotype is associated with an altered expression of the gene.
gene-disease association linked with post-translational modification
A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product.
methylation or phosphorylation of protein product
regulation of transcription
A process that modulates the frequency, rate or extent of transcription.
regulation of translation
A process that modulates the frequency, rate or extent of translation.
regulation of molecular quantity
A process that modulates the frequency, rate or extent of process involved in the creation or destruction of a molecule.
regulation of molecular production
A process that modulates the frequency, rate or extent of process involved in the production of a molecule.
regulation of molecular degradation
A process that modulates the frequency, rate or extent of process involved in the destruction of a molecule.
protein mediated regulation of translation
A process mediated by a protein that modulates the frequency, rate or extent of translation.
rna mediated regulation of translation
A process mediated by rna that modulates the frequency, rate or extent of translation.
process maintenance
The process of maintaining some the frequency, rate or extent of another process.
increased frequency of process from increased regulation
The increase of regulation leads to a increased occurence of processes of the target type.
decreased frequency of process from increased regulation
The increase of regulation leads to a decreased occurence of processes of the target process type.
regulation of process frequency
regulation of a process duration is a process that modulates the frequency of another process relative to some reference process.
regulation of process duration
regulation of a process duration is a process that modulates the duration of another process relative to some reference process.
increased duration of process from increased regulation
increased duration of process from increased regulation is a process in which the duration of the target process is increased as a result of increased regulation.
decreased duration of process from increased regulation
decreased duration of process from increased regulation is a process in which the duration of the target process is decreased as a result of increased regulation.
regulation of process spatial extent
heating the solution causes greater diffusion of a chemical.
regulation of a process spatial extent is a process that modulates the spatial extent of another process relative to some reference process.
increased spatial extent of process from increased regulation
The increase of regulation leads to a increased spatial extent of the target process.
decreased spatial extent of process from decreased regulation
The increase of regulation leads to a decreased spatial extent of the target process.
maintenance of spatial extent of process
maintenance of spatial extent of process is a regulation of a process' spatial extent within some specified parameter.
maintenance of duration of process
maintenance of duration of process is a process that regulates a target process to maintain its duration within an expected interval.
maintenance of frequency of process
maintenance of frequency of process is a process that regulates the number of occurences of a target process type to a specified number or interval.
regulation of object quantity
regulation of a participant quantity is the regulation of a process in which the quantity of its partcipants is changed.
increased object production from increased regulation
increased regulation leads to an increase in the number of target objects of a specified type.
decreased object production from increased regulation
increased regulation leads to a decrease in the number of target objects of a specified type.
increased object consumption from increased regulation
increased regulation leads to an increase in the consumption of an object of specified type.
decreased object consumption from increased regulation
increased regulation leads to an decrease in the consumption of an object of specified type.
regulation of object consumption
A process that modulates the frequency, rate or extent of process involved in the consumption of an object.
regulation of object production
regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is increased.
maintenance of quantity of object production
maintenance of quantity of object production is a regulation of object production in which the number of objects produced is held more or less constant.
maintenance of level of object consumption
regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is maintained at a steady level.
number of objects produced
number of objects produced is a count of objects that were produced in some process.
number of objects consumed
number of objects consumed is a count of objects that were consumed in some process.
difference in number of objects produced
A difference in number of objects produced is a count of the number of objects produced with respect to a second variable (space, time, etc)
increase in number of objects produced
An increase in the number of objects produced is the positive value of a difference in number of objects produced.
decrease in number of objects produced
An decrease in the number of objects produced is the negative value of a difference in number of objects produced.
user account
user account allows a user to authenticate to system services and be granted authorization to access them.
annotation
An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information.
comment
A comment is a verbal or written remark often related to an added piece of information, or an observation or statement.
audio recording
An audio recording is an electrical or mechanical inscription and re-creation of sound waves, such as spoken voice, singing, instrumental music, or sound effects.
issue
An issue is a single instance of a periodically published journal, magazine, or newspaper.
slideshow
A slideshow is a visual presentation of information contained within a collection of slides.
database cross-reference
A database cross-reference is an association between one data item and another.
exact cross-reference
An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source).
double stranded DNA
double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids.
nucleic acid strand
A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex.
positive nucleic acid strand
The positive nucleic acid strand refers to the strand that is to be read 5' to 3'.
forward strand
negative nucleic acid strand
The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'.
reverse strand
double stranded nucleic acid
double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids.
double stranded RNA
double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids.
full agreement
full agreement is the result of consensus decision making when members of the group unanimously agree.
mass spectrometry experiment
A mass spectrometry experiment is an experiment that involves the use of a mass spectrometer.
full disagreement
full agreement is the result of consensus decision making when members of the group unanimously disagree.
ribosomal RNA gene
A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule.
statement
A statement is a proposition that is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts.
slope
A slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline. Slope is normally described by the ratio of the "rise" divided by the "run" between two points on a line.
software process identifier
A software process identifier is an identifier for a software process in some operating system.
hypothetical
hypothetical is the quality of an entity that is conjectured to exist.
database row
A database row is a row that is part of a database table.
SADI semantic web service
a SADI semantic web service is a semantic web service that follows the SADI specification
semantic web service
a semantic web service is a web service that provides a formal, machine understanble description of its functionality.
REST web service
a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification.
SOAP web service
a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP).
web service invocation
A web service invocation involves the execution of a web service.
SADI web service invocation
A SADI web service invocation is the excution of a SADI web service.
media
media are audo/visual/audiovisual modes of communicating information for mass consumption.
behaviour
Behaviour is the set of actions and mannerisms made by systems (biological or otherwise) in response to stimuli or inputs, whether internal or external, conscious or subconscious, overt or covert, and voluntary or involuntary.
history
history is a sequence of past events.
structural motif
A structural motif is a pattern in a structure formed by the spatial arrangement of atoms.
consensus
consensus is an acceptable resolution, one that can be supported, even if not the preferred outcome for each individual.
increased molecular degradation from increased regulation
A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation.
decreased molecular degradation from decreased regulation
A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation.
increased molecular degradation from decreased regulation
A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation.
decreased molecular degradation from increased regulation
A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation.
increased molecular production from increased regulation
A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation.
decreased molecular production from increased regulation
A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation.
increased molecular production from decreased regulation
A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation.
decreased molecular production from decreased regulation
A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation.
increased chemical destruction
increased chemical destruction is a process in which there is an increase in the amount of chemical destroyed relative to some reference process
decreased chemical destruction
decreased chemical destruction is a process in which there is a decrease in the amount of chemical destroyed relative to some reference process
assertional qualifier
An assertional qualifier is the quality of affirmation, either being positive or negative.
positive
positive is an assertional qualifier that expresses the validity or truth of a basic assertion.
negative
negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion.
intensity
intensity is a quality that represents the strength or degree of something.
mild
mild is a qualitative intensity value that is more intense than weak, but less intense than moderate.
moderate
moderate is a qualitative intensity value that is more intense than mild, but less intense than strong.
severe
severe is a qualitative intensity value that is more intense than strong, but less intense than fatal.
fatal
fatal is a qualitative intensity value that is more intense than severe, leading to the death/non-functioning of a system.
strong
strong is a qualitative intensity value that is more intense than moderate, but less intense than severe.
weak
weak is a qualitative intensity value that is more intense than none, but less intense than mild.
to test a hypothesis
to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence.
to characterize
to characterize is the capability to classify the attributes or features of an entity against a reference classification.
to describe
to describe is the capabilty to communicate facts about an entity.
5' splice site
The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised.
3' splice site
The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised.
amino acid
An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom.
cis regulatory element
A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects.
trans-regulatory element
A trans-regulatory element is a DNA sequence associated with the regulation of a gene located outside the genomic region supporting the corresponding structural DNA region of the trans-regulatory element (i.e., a different DNA strand or different chromosome).
small cytoplasmic RNA (scRNA) gene
A small cytoplasmic RNA (scRNA) gene is a gene that encodes a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
small nuclear RNA (snRNA) gene
A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule.
small nucleolar RNA (snoRNA) gene
A small nucleolar RNA (snoRNA) gene is a gene that encodes a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
transfer RNA (tRNA) gene
A transfer RNA (tRNA) gene is a gene that codes for a tRNA used in the translation of a messenger RNA (mRNA) to produce a protein product.
solube RNA (sRNA) gene
tRNA gene
small cytoplasmic RNA (scRNA)
A small cytoplasmic RNA (scRNA) molecule is a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
scRNA
transfer RNA (tRNA)
A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product.
tRNA
small nuclear RNA (snRNA)
A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell.
snRNA
small nucleolar RNA (snoRNA)
A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
snoRNA
non-protein coding RNA (ncRNA)
A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product.
data collection device
A data collection device is a device that collects information about one or more objects.
mass spectrometer
A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field.
microarray device
A microarray device is a device that identifies the binding of a target substance to a physically immobile substrate placed in an array or lattice.
microarray platform
to identify
to identify is the capability to determine the identity of something.
nmr device
A nuclear magnetic resonance (NMR) device is a device that applies a magnetic field to perturb nuclei with an odd number of protons and/or of neutrons in order to hav them absort and re-emit electromagnetic radiation.
nuclear magnetic resonance device
catalog
A catalog is a systemic collection of items of the same type.
registry
likelihood
Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome.
log likelihood
Log likelihood is the natural logarithm of the likelihood function
standard score
A standard score is the (signed) number of standard deviations an observation or datum is above the mean.
z-value, z-score, normal score, standardadized variable.
The set of all numbers x satisfying 0<=x<=1 is an interval which contains 0 and 1, as well as numbers between them.
an interval is a set of real numbers with the property that any number that lies between thwo numbers in the set is also included in the set.
open interval
(0,1) is an open interval that is greater than 0 and less than 1.
an open interval is an interval that does not include its endpoints.
closed interval
A closed interval is an interval that includes its endpoints, and is denoted with square brackets.
[0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1.
chemical-pathway association
a chemical-pathway association is an association between a chemical and a pathway.
drug-pathway association
left open interval
a left open interval is an interval in which there is no element that is smaller than all other elements.
right open interval
a right open interval is an interval in which there is no element that is greater than all other elements.
right closed interval
a right closed interval is an interval in which there is a real number that is larger than all of its elements.
left closed interval
a left closed interval is an interval in which there is a real number that is smaller than all its elements.
pharmacokinetic pathway
a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule.
pharmacodynamic pathway
a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway.
chemical-gene assocation
a chemical-gene assocation is an assocation between a chemical and a gene.
set item
set item is an item in a set.
collection item
a collection item is an item in a collection.
list item
ordered list item
an ordered list item is an item in an ordered list.
anatomical entity
an anatomical entity is an object that is a structural part (material or immaterial) of a biological entity.
ovopub
An ovopub is an information content entity that contains and links to one or more resources and/or statements, including those describing its provenance, and is itself a dereferenceable resource.
collection ovopub
A collection ovopub is an ovopub that contains and links to one or more assertion subgraphs and/or ovopubs, as well as statements describing its provenance. It is used to share a specific set of items or restrict a search to the resources contained therein.
assertion ovopub
An assertion ovopub is an ovopub that contains and links to an assertion subgraph with one or more statements that may be true or false, as well as statements describing its provenance.
organism
A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not).
cell
A cell is a biological entity that is contained by a plasma membrane.
tissue
A tissue is a mereologically maximal collection of cells that together perform some function.
organ
An organ is a collection of tissues joined in structural unit to serve a common function.
chemical entity
A chemical entity is a material entity that pertains to chemistry.
atom, ion, molecule, chemical substance,
weak submolecular component
A weak submolecular component is a submolecular component that weakly connects submolecular components.
polypeptide
A polypeptide is an organic polymer composed of amino acid residues.
nucleic acid
A nucleic acid is an organic polymer composed of a sequence of nucleotide residues.
ribonucleic acid
A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues.
deoxyribonucleic acid
A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues.
lipid
A lipid is a water-insoluable organic molecule.
chemical interaction
A chemical interaction is a biochemical process in which chemical entities interact through some set of attractive forces.
primary structure descriptor
A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology.
protein sequence
A protein acid sequence is the character representation of the molecular structure of a protein.
amino acid sequence
polypeptide sequence
nucleic acid sequence
A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid.
ribonucleic acid sequence
A ribonucleic acid sequence is a symbolic representation of the sequence of ribonucleic acid residues in a ribonucleic acid.
RNA sequence
deoxyribonucleic acid sequence
A deoxyribonucleic acid sequence is a symbolic representation of the sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid.
DNA sequence
biological data
biological data is scientific data relevant to biology.
submolecular entity
A submolecular entity is a part of a molecular entity.
secondary structure descriptor
A secondary structure descriptor describes local topological patterns in a biopolymer.
tertiary structure descriptor
A tertiary structure descriptor describes 3D topological patterns in a biopolymer.
quaternary structure
A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex.
oligosaccharide
An oligosaccharide is an organic polymer composed of monosaccharides joined by glycosidic bonds.
genetic polymorphism
genetic polymorphism is the description of a difference in genetic composition at some location.
snp
single nucleotide polymorphism
single nucleotide polymorphism (SNP) is a variation in a single base in the genetic composition between different individuals of the same species.
genetic data
genetic data is data pertaining to genetics.
biological sex
biological sex is the quality of a biological organism based on reproductive function or organs.
monosaccharide
A monosaccharide is an organic polymer that consists of a single polyhydroxy aldehyde or ketone group.
PDB chain identifier
A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank .
PDB record identifier
A PDB record identifier is an identifier for a PDB generated record.
hydrogen bond
A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom.
cation pi interaction
A cation pi interaction is an ionic interaction between the localized negative charge of π orbital electrons, located above and below the plane of an aromatic ring, and a positive charge.
gene
A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript.
biochemical reaction
A biochemical reaction is a biochemical process that involves the conversion of at least one chemical participant (target) into another (product) by an enzyme (agent).
chemical element
A chemical element is a (effectively) homogeneous substance composed of one type of atom.
drug
A drug is a chemical entity that regulates a biological process.
pharmaceutical preparation
A pharmaceutical preparation is a chemical substance approved for use in the medical diagnosis, cure, treatment, or prevention of disease.
binding site
A binding site is a molecular site which when occupied with particular ligands leads to structural transformations that initiatiate new moelcular processes.
active site
An active site is a molecular site in which a chemical event occurs (structural transformation or conformational change).
haplotype
A haplotype is one of a set of genomic sequence variants.
protein
A protein is an organic polymer that is composed of one or more linear polymers of amino acids.
atom
An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons.
base pair
A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases.
biological entity
A biological entity is a heterogeneous substance that contains genomic material or is the product of a biological process.
strong submolecular component
A strong submolecular component is a submolecular component that strongly connects submolecular components.
male
male is a biological sex of an individual with male sexual organs.
molecular site
A moleclar site is a spatial region bounded (in part or in whole) by a molecule and may be occupied by other material entities (e.g. drugs).
allosteric site
An allosteric site is a binding site that when bound to particular ligand changes the conformational state and affects its functionality.
biological fluid
A biological fluid is a fluid of biological origin.
female
female is a biological sex of an individual with female sexual organs.
evolutionary lineage
evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species.
cell line
A cell line is a collection of genetically identifical cells.
strain
A strain is a genetic variant or kind of microorganism.
phenotype
A phenotype is an observable characteristic of an individual.
life status
life status is the quality of whether something is alive or dead.
alive
alive is the state of a biological organism that exhibits biological functions.
dead
dead is the quality of an object in which there is a cessation of all biological functions.
family history
family history is the systematic narrative and research of past events relating to a specific family, or specific families.
generation number
generation number is a count of the number of biological reproduction events elapsed from some starting reference point.
5' untranslated region
The five prime untranslated region (5' UTR) is a section of messenger RNA (mRNA) and the DNA that codes for it that starts at the +1 position (where transcription begins) and ends one nucleotide before the start codon (usually AUG) of the coding region.
bioinformatic data
bioinformatic data is data genereated or used for computer-based investigations of biological phenomena.
sequence alignment
A sequence alignment is the character-based alignment of sequences using some method.
multiple sequence alignment
A multiple sequence alignment is a sequence alignment involving more than two sequences.
pairwise sequence alignment
A pairwise sequence alignment is the alignment of exactly 2 sequences.
3' untranslated region
A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon.
organic submolecule
An organic submolecule is connected region of a molecule.
organic molecule
An organic molecular entity is a chemical entity composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen)
open reading frame
An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon.
amino acid residue
An amino acid residue is a part of a molecule that is derived from an amino acid molecule.
nucleotide residue
A nucleotide residue is a part of a molecule that derives from a nucleotide.
poison
A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity.
active ingredient
An active ingredient is a molecular entity that exhibits biological activity.
operon
An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA.
gene regulatory component
A gene regulatory component is a gene component that exerts a regulatory function.
gene enhancer
A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster.
inactive ingredient
Aninactive ingredient is a molecular entity that does not exhibit biological activity.
to serve as a template for molecular synthesis
to serve as a template for molecular synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which another molecule may be produced.
to serve as a template for protein synthesis
to serve as a template for protein synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a protein may be produced.
to serve as a template for RNA synthesis
to serve as a template for RNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which an RNA molecule may be produced.
to serve as a template for DNA synthesis
to serve as a template for DNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a DNA molecule may be produced.
deoxyribonucleic acid template
A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription.
deoxyribonucleic acid primer
A deoxyribonucleic acid primer is a deoxyribonucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.
to serve as a primer for DNA synthesis
to serve as a primer for DNA synthesis is the capability of a short nucleic acid to bind to the 5' end of single strand of DNA template and help initiate DNA replication.
RNA transcript component
An RNA transcript component is a region of an RNA transcript.
mature mRNA
A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.
pre-mRNA
Precursor mRNA (pre-mRNA) is a single strand of messenger ribonucleic acid (mRNA) that is synthesized from a DNA template throught transcription.
mRNA splice variant
An mRNA splice variant is an mRNA molecule that varies from another mRNA molecule of the same gene origin but having a different final sequence due to differences in its assembly from splice sites.
messenger RNA
A messenger RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.
dna gene
A gene that is located on DNA.
rna gene
A gene that is located on RNA.
allele
An allele is one of a set of sequence variants of a gene.
ploidy
ploidy is the cellular quality relating to the amount of DNA contained in a cell.
chemical transport
chemical transport is the directed movement of a chemical entity by some agent (e.g. transporter).
active transport
active transport is the movement of a substance across a membrane against its concentration gradient (from low to high concentration) and requires chemical energy.
molecular complex formation
molecular complex formation is the process of forming a molecular complex from its constituent parts.
molecular complex dissociation
molecular complex disassociation is the process of dissambly of a molecular complex into its constitutent parts.
regulation of biochemical process
regulation of biochemical process is a process that changes the frequency, rate or extent of a target biochemical process.
biochemical activation
biochemical activation is a molecular interaction that increases the catalytic rate of the target enzyme.
biochemical inhibition
biochemical inhibition is a molecular interaction that decreases the catalytic rate of the target enzyme.
process up-regulation
positive regulation
process up-regulation is a process that increases the frequency, rate or extent of one or more processes in relation to a reference state.
process down-regulation
negative regulation
process down-regulation is a process that decreases the frequency, rate or extent of one or more processes in relation to a reference state.
medical data
medical data is data of interest to medicine.
disease
disease is the outward manifestation of one or more disorders.
transcription
transcription is the process of creating a complementary RNA copy of a sequence of DNA.
translation
translation is the process of producing a polypeptide from a ribonucleic acid by a ribosome.
molecular modification
Molecular modification is chemical alteration of a known and previously characterized lead compound for the purpose of enhancing its usefulness as a drug. This could mean enhancing its specificity for a particular body target site, increasing its potency, improving its rate and extent of absorption, modifying to advantage its time course in the body, reducing its toxicity, changing its physical or chemical properties (like solubility) to provide desired features.
metabolism
Metabolism is the set of chemical processes that occur within a living organism in order to maintain life.
catabolism
Anabolism is the set of metabolic processes that take apart larger chemical entities units into smaller chemical entities.
anabolism
Anabolism is the set of metabolic processes that construct larger chemical entities units from smaller chemical entities.
carbohydrate residue
A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule.
nucleic acid part
A nucleic acid part is a component of a nucleic acid.
deoxyribonucleotide residue
A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide.
ribonucleotide residue
A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide.
pharmaceutical component
A pharmaceutical component is a part of a pharmaceutical preparation.
to covalently modify
to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms.
covalently connected entity
A covalently connected molecular entity is the mereological sum of a collection of covalently bonded atoms.
chemical complex
A chemical complex is a chemical entity composed of a weakly connected ions or molecules.
enzyme
An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction.
catalyst
A catalyst is a molecule that has the capability to reduce the activation energy of a reaction and hence increase the overall rate of reaction.
chemical reaction
A chemical reaction is a process that leads to the transformation of one set of chemical substances to another.
organic polymer
An organic polymer is an organic molecule composed of connected set of monomeric units.
to modify conformation of
to modify conformation of is to affect the spatial arrangement of an entity.
to cleave
to cleave is to split or sever an object along a natural line or grain.
to combine
to combine is the capability to modify a set of objects in a way that the object is merged with another object to form a new object or substance.
to breathe
to breathe is the capability to inhale and exhale air into the body during respiration.
to conformationally activate
to conformationally activate is to modify the conformation of an entity in such a way that it becomes activated or functional.
to conformationally inhibit
to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited.
to oxidize
to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity.
to reduce
to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity.
to modify oxidation state of
to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion.
substrate
A substrate is a molecule that is consumed in the course of a biochemical reaction.
product
to be modified
to be modified is the capability to be actively interacted with in such a way that it leads to a physical reconfiguration.
to be cleaved
to be cleaved is the capability to be modified in a way that splits one part of the object from the other.
to be covalently modified
to be covalently modified is the capability of a chemical entity to have bonds added or removed
to be combined
to be combined is the capability to be modified in a way that the object is merged with another object to form a new object or substance.
to be transported
to be transported is the disposition to undergo motion.
to be electronically modified
to be electronically modified is the capability of a chemical entity to have electrons added or removed.
to gain an electron
to gain an electron is the capability of a chemical entity to receive an electron.
to lose an electron
to lose an electron is the capability of a chemical entity to lose an electron.
to be activated
to be activated is the capability to be modified in such a way that the conformational change leads to an increase in another capability.
to be inhibited
to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability.
to be conformationally changed
to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed.
multicellular organism
A multi-cellular organism is an organism that consists of more than one cell.
unicellular organism
A unicellular organism is a organism that is composed of a single cell.
cellular organism
A cellular organism is an organism that contains one or more cells.
non-cellular organism
A non-cellular organism is an organism that does not contain a cell.
virus
A virus is a non-cellular organism that can replicate only inside the living cells of an organism.
drug regulatory authority
A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals.
specialized material entity
A specialized material entity is a material entity that is defined by having some quality, role or capability.
reagent
A reagent is a substance that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs.
specimen
A specimen is a portion of material for use in testing, examination, or study.
pathogen
A pathogen or infectious agent is a microorganism that causes disease in its host.
host
A host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter.
buffer
A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base.
solvent
A solvent is a substance that can dissolve other substances (solutes).
solute
A solute is a substance that becomes dissolved in a solvent.
antigen
An antigen is a chemical entity that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor.
receptor
A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal.
target
centrifugation pellet
A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge.
supernatant
A supernatent is a liquid substance that remains after centrifugation.
centrifugation substance
A centrifugation substance is a substance that is the target or product of centrifugation.
liquid solution component
A liquid solution component is a part of a liquid solution.
evaluation role
An evaluation role is a processual role held by an entity during some evaluation.
placebo
A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient.
test role
A test role is the role of an individual that is a participant in the study and is the target of the intervention.
control role
A control role is the role of an individual that is part of a study, but is not subject to the intervention that is to be tested.
ligand
A ligand is a molecule that is part of a complex by weakly interacting with another molecule.
low barrier hydrogen bond
A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms.
activator
A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality.
inhibitor
A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality.
molecular regulator
A molecular regulator is a molecule that regulates the function of another chemical entity.
signal transducer
A signal transducer is a molecule that responds to and amplifies a signal in a signalling system.
signal
A signal is an object that initiates a sequence of events.
messenger
A mesenger is a molecule involved in either signal detection or signal propagation from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.
second messenger
A second messenger is a molecule that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.
submolecule
A submolecule is a mereological sum of covalently bonded atoms.
charge quality
charge quality is the quality pertaining to electric charge.
intron
An intron is a region of a gene that is removed from the final protein open reading frame.
gene component
A gene component is a component of a gene.
exon
An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing.
gene promoter
A gene promoter is a region of DNA that initiates transcription of a particular gene.
start codon
A start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon is almost always preceded by an untranslated region 5' UTR.
stop codon
A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.
RNA transcript
An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template.
splice site
A splice site is a region required for the excision of an intron and connection to another exon.
molecular pocket
A molecular pocket is a site on a molecule that appears as a depression into the structure.
acid
An acid is a molecular entity in solution capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
base
A base is a molecular entity dissolved in a solvent that is capable of accepting a proton (Bronsted base) or forming a covalent bond with a hydron (Lewis base) .
isomer
An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity.
ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge.
cation
An anion is an atom or molecule with a net positive electrical charge.
anion
An anion is an atom or molecule with a net negative electrical charge.
polar solvent
A polar solvent is a solvent that exhibits a polar quality.
nonpolar solvent
A non-polar solvent is a solvent that exhibits a non-polar quality.
positive charge
A positive charge is a charge where the value is positive.
heterogeneous substance
A heterogeneous substance is a chemical substance that is composed of more than one different kind of component.
homogeneous substance
A homogeneous substance is a substance that is composed of a uniform type of entity.
negative charge
A negative charge is a charge where the value is negative.
antibody
An antibody (also known as immunoglobulins, abbreviated Ig) are gamma globulin proteins that are used by the immune system to identify and neutralize foreign objects. They are typically made of two large heavy chains and two small light chains.
alpha helix
An alpha helix is structural region of a protein that is characterized by 3.6 residues per turn, a translation of 1.5 angstroms along the helical axis in which backbone N-H groups form a hydrogen bond to the backbone carboxyl group of the amino acid four residues prior.
beta strand
A beta strand is structural region of a protein that is characterized by a roughly planar sequence of amino acid residues forming hydrogen bonds between the N-O and the C=O of another part of the peptide and having their side chains perpendicular to the planar axis.
protein part
A protein part is any submolecule of a protein.
ionic interaction
An ionic interaction is a weak submolecular interaction between a charged submolecules.
protein complex
A protein complex is a molecular complex composed of at least two polypeptide chains.
single bond
A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared.
double bond
A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared.
triple bond
A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared.
aromatic bond
An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared.
disulfide bond
A disulfide bond is a bond between two sulfur atoms.
dipole-dipole interaction
A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms.
van der Waals interaction
van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole.
base stack
A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces.
molecular complex
A molecular complex is a chemical complex composed of weakly interacting molecular entities, and excludes bulk solvent.
acid-base reaction
An acid-base reaction is a chemical reaction between an acid and a base.
catalyzed reaction
A catalyzed reaction is a chemical reaction that is facilitated by a catalyst.
redox reaction
A redox reaction is a chemical reaction in which there is a net movement of electrons from one reactant to another.
inorganic reaction
An inorganic reaction is a chemical reaction that involves the transformation of inorganic molecules.
decomposition reaction
A decomposition reaction is an inorganic reaction in which molecule is fragmented into submolecules or atoms.
displacement reaction
A displacement reaction is an inorganic reaction in which a elementary substance displaces and sets free a constituent atom from a molecule.
double displacement reaction
A double displacement reaction is a displacement reaction in which two molecules swap ions, effectively displacing each other to form two new molecules.
single displacement reaction
A single displacement reaction where one atom is transferred out of one molecule and into another.
synthesis reaction
A synthesis reaction is an inorganic reaction in which two or more molecules are chemically bonded together to produce a single product.
organic reaction
An organic reaction is a chemical reaction involving at least one organic molecule.
isomerization reaction
An isomerization reaction is a chemical reaction in which a molecule is converted into its isomer.
addition reaction
An addition reaction is an organic reaction where two or more molecules combine to form a larger one. Addition reactions are limited to chemical compounds that have multiply-bonded atoms: * Molecules with carbon-carbon double bonds or triple bonds * Molecules with carbon - hetero double bonds like C=O or C=N
polar addition reaction
A polar addition reaction is an addition reaction involving polar residues.
non-polar addition reaction
A non-polar addition reaction is an addition reaction involving non-polar residues.
free radical addition
A free radical addition is a non-polar addition reaction involving free radicals.
nucleophilic addition reaction
A nucleophilic addition reaction is an addition reaction where a pi bond is removed by the creation of two new covalent bonds by the addition from a nucleophile.
electrophilic addition reaction
An electrophilic addition reaction is a polar addition reaction where a pi bond is removed by the creation of two new covalent bonds.
biochemical pathway
A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome.
chemical reaction pathway
A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product.
chemical synthesis pathway
A chemical synthesis pathway is a pathway involved in the assembly of a chemical.
chemical degradation pathway
A chemical degradation pathway is a pathway involved in the disassembly of a chemical.
3d structure model
A 3D structure model is a representation of the spatial arrangement of one or more chemical entities.
sequence profile
A sequence profile is provides the preference for a character at each position of an abstracted sequence.
metabolic pathway
A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products.
regulatory pathway
A regulatory pathway is a series of biochemical reactions that lead to the increase or decrease of activity of participating molecular components.
medical history
A medical history is a record of the events of a recipient of medical care.
binary compound
A binary compound is a mereological maximum sum of two kinds of weakly connected entities.
stereoisomer
A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms.
diastereomer
A diastereomer is a stereoisomer that is not a mirror image of its isomer.
enantiomer
An enantiomer is a stereoisomer that is a mirror image of its isomer.
optical isomer
An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light.
structural isomer
A structural isomer is an isomer in which the atoms are joined together in different ways.
ring
A ring is a submolecule with a circular topology.
aromatic ring
An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring.
heterocyclic ring
A heterocyclic ring is a ring containing a hetero atom.
homocyclic ring
A homocyclic ring is a ring where the atoms are of a single type.
ionic compound
An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions.
allotrope
An allotrope is a structural variant of a chemical element.
carbon allotrope
A carbon allotrope is a chemical substance composed of carbon.
diamond
diamond is a carbon allotrope in which each carbon atom in diamond is covalently bonded to four other carbons in a tetrahedron. These tetrahedrons together form a 3-dimensional network of puckered six-membered rings of atoms.
graphite
graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon.
fullerene
fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube.
aggregated carbon nanorods
aggregate of carbon nanorods is an allotrope of carbon considered to be the least compressible material known, as measured by its isothermal bulk modulus; aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), while a conventional diamond has a modulus of 442 GPa. ADNRs are also 0.3% denser than regular diamond.
amorphous carbon
amorphous carbon is an allotrope of carbon that does not have any crystalline structure. As with all glassy materials, some short-range order can be observed, but there is no long-range pattern of atomic positions.
carbon nanofoam
carbon nanofoam is an allotrope of carbon that consists of a low-density cluster-assembly of carbon atoms strung together in a loose three-dimensional web. Each cluster is about 6 nanometers wide and consists of about 4000 carbon atoms linked in graphite-like sheets that are given negative curvature by the inclusion of heptagons among the regular hexagonal pattern.
chaoite
chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white.
glassy carbon
glassy carbon is an allotrope of carbon which is widely used as an electrode material in electrochemistry, as well as for high temperature crucibles and as a component of some prosthetic devices.
ionsdaleite
ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond.
boron atom
carbon atom
hydrogen atom
helium atom
lithium atom
beryllium atom
nitrogen atom
oxygen atom
fluorine atom
neon atom
sodium atom
magnesium atom
aluminium atom
silicon atom
phosphorus atom
sulfur atom
chlorine atom
argon atom
potassium atom
calcium atom
scandium atom
titanium atom
vanadium atom
chromium atom
manganese atom
iron atom
cobalt atom
nickel atom
copper atom
zinc atom
gallium atom
germanium atom
arsenic atom
selenium atom
bromine atom
krypton atom
rubidium atom
strontium atom
yttrium atom
zirconium atom
niobium atom
molybdemum atom
technetium atom
ruthenium atom
rhodium atom
palladium atom
silver atom
cadmium atom
indium atom
tin atom
antimony atom
tellurium atom
iodine atom
xenon atom
caesium atom
barium atom
lanthanum atom
hafnium atom
tantalum atom
tungsten atom
rhenium atom
osmium atom
iridium atom
platinum atom
gold atom
mercury atom
thallium atom
lead atom
bismuth atom
polonium atom
astatine atom
radon atom
francium atom
radium atom
actinium atom
rutherfordium atom
dubnium atom
seaborgium atom
bohrium atom
hassium atom
meitnerium atom
darmstadtium atom
roentgenium atom
copernicium atom
unutrium atom
ununquadium atom
ununpentium atom
ununhexium atom
ununseptium atom
ununoctium atom
cerium atom
praseodymium atom
neodymium atom
promethium atom
samarium atom
europium atom
gadolinium atom
terbium atom
dysprosium atom
holmium atom
erbium atom
thulium atom
ytterbium atom
lutetium atom
thorium atom
protactinium atom
uranium atom
neptunium atom
plutonium atom
americium atom
curium atom
berkelium atom
californium atom
einsteinium atom
fermium atom
mendelevium atom
nobelium atom
lawrencium atom
covalent bond
A covalent bond is a strong submolecular interaction between atoms.
biomolecular structure descriptor
A biomolecular structure descriptor is structure description for organic compounds.
molecular structure file
A molecular structure file is a file that contains a description of molecular structure.
molecular structure descriptor
molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity.
chemical data
A chemical datum is a scientific data item which conforms to some specification, either for how it is calculated or for how it is measured, and is commonly used in the domain of chemistry to name and differentiate different numeric properties (both calculated and measured) which are about chemical entities.
molecule
A molecule is the mereological maximal sum of a collection of covalently bonded atoms.
chemical substance
A chemical substance is a chemical complex of weakly interacting molecular entities, and may include bulk solvent.
PDB file
A PDB file is a molecular structure file specified by the Protein DataBank (PDB).
collection of 3d molecular structure models
A collection of 3D molecular structure models is just that.