OBO Relations Ontology
type: Ontology
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
source: ro
imports: annotations.owl
imports: core.owl
imports: el-constraints.owl
imports: go-biotic.owl
imports: go mf import.owl
imports: pato import.owl
imports: rohom.owl
imports: temporal-intervals.owl
version IRI: ro.owl

IAO_0000426
IAO_0000115: An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
sub property of: logical macro assertion on an object property

OBO foundry unique label
IAO_0000114: pending final vetting

RO_0001900
IAO_0000115: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

never in taxon
type: AnnotationProperty
IAO_0000117: Chris Mungall
IAO_0000112: tooth SubClassOf 'never in taxon' value 'Aves'
IAO_0000425: ?X DisjointWith RO_0002162 some ?Y
IAO_0000115: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
sub property of: taxonomic class assertion
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

mutually spatially disjoint with
type: AnnotationProperty
IAO_0000115: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
IAO_0000118: shares no parts with
IAO_0000118: non-overlapping with
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
sub property of: logical macro assertion on a class
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

taxonomic class assertion
type: AnnotationProperty
IAO_0000115: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
sub property of: logical macro assertion on a class

ambiguous for taxon
type: AnnotationProperty
IAO_0000115: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
sub property of: taxonomic class assertion

dubious for taxon
type: AnnotationProperty
comment: This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
IAO_0000115: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
sub property of: taxonomic class assertion
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

present in taxon
type: AnnotationProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000115: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
sub property of: taxonomic class assertion
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

logical macro assertion
type: AnnotationProperty
IAO_0000115: An assertion that holds between two classes that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

annotation property cardinality
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
sub property of: logical macro assertion on an annotation property
range: nonNegativeInteger

logical macro assertion on a class
type: AnnotationProperty
IAO_0000115: A logical macro assertion whose domain is an IRI for a class
sub property of: logical macro assertion

logical macro assertion on a property
type: AnnotationProperty
IAO_0000115: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty
sub property of: logical macro assertion on a property

dispositional interpretation
type: AnnotationProperty
IAO_0000115: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
sub property of: logical macro assertion on an object property

has no connections with
type: AnnotationProperty
IAO_0000118: shares no connection with
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
IAO_0000115: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
IAO_0000112: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
IAO_0000115: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
sub property of: inherited annotation property

always present in taxon
type: AnnotationProperty
IAO_0000112: brain always_present_in_taxon 'Vertebrata'
IAO_0000118: never lost in
IAO_0000115: S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
IAO_0000112: forelimb always_present_in_taxon Euarchontoglires
IAO_0000116: This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
sub property of: present in taxon

temporal logical macro assertion on a class
type: AnnotationProperty
IAO_0000232: This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
sub property of: logical macro assertion on a class

measurement property has unit
type: AnnotationProperty
sub property of: logical macro assertion on an annotation property

has start time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

has end time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

start, days post fertilization
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
sub property of: has start time value

end, days post fertilization
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
sub property of: has end time value

start, years post birth
type: AnnotationProperty
IAO_0000115: Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
sub property of: has start time value

end, years post birth
type: AnnotationProperty
IAO_0000115: Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
sub property of: has end time value

start, months post birth
type: AnnotationProperty
IAO_0000115: Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
sub property of: has start time value

end, months post birth
type: AnnotationProperty
IAO_0000115: Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
sub property of: has end time value

month of gestation
type: AnnotationProperty
IAO_0000115: Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
sub property of: temporal logical macro assertion on a class

has developmental stage marker
type: AnnotationProperty
IAO_0000115: A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
sub property of: temporal logical macro assertion on a class

start, days post coitum
type: AnnotationProperty
IAO_0000232: For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
IAO_0000115: Count of number of days intervening between the start of the stage and the time of coitum.
sub property of: has start time value

end, days post coitum
type: AnnotationProperty
IAO_0000115: Count of number of days intervening between the end of the stage and the time of coitum.
sub property of: has end time value

start, weeks post birth
type: AnnotationProperty
sub property of: has start time value

end, weeks post birth
type: AnnotationProperty
sub property of: has end time value

is asymmetric relational form of process class
type: AnnotationProperty
IAO_0000115: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
sub property of: is relational form of process class

is symmetric relational form of process class
type: AnnotationProperty
IAO_0000115: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
sub property of: is relational form of process class

is relational form of process class
type: AnnotationProperty
IAO_0000115: R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
sub property of: is relational form of a class

is direct form of
type: AnnotationProperty
creator: Chris Mungall
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
IAO_0000116: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
IAO_0000115: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
IAO_0000115: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion

is a defining property chain axiom
type: AnnotationProperty
IAO_0000115: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
sub property of: logical macro assertion on an axiom

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
IAO_0000115: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
sub property of: is a defining property chain axiom

is relational form of a class
type: AnnotationProperty
IAO_0000115: An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
sub property of: logical macro assertion on an object property

eco subset
type: AnnotationProperty
sub property of: subset_property

subset_property
type: AnnotationProperty

in_subset
type: AnnotationProperty

in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000426: (forall (?x ?y) (iff (neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (or (synapsed_by ?x ?y) (synapsed_to ?x ?y))))) (forall (...s ?x ?y ?z) (iff (neural_circuit_path ...s ?x ?y ?z) (and (neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (or (synapsed_by ?y ?z) (synapsed_to ?y ?z))))) (forall (?x ?y) (iff (in_neural_circuit_with ?x ?y) (exists (...s) (neural_circuit_path ?x ...s ?y))))
IAO_0000115: A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
IAO_0000117: David Osumi-Sutherland
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

upstream in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000426: (forall (?x ?y) (iff (upstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_to ?x ?y)))) (forall (...s ?x ?y ?z) (iff (upstream_neural_circuit_path ...s ?x ?y ?z ) (and (upstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_to ?y ?z)))) (forall (?x ?y) (iff (upstream_in_neural_circuit_with ?x ?y) (exists (...s) (upstream_neural_circuit_path ?x ...s ?y))))
IAO_0000115: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
IAO_0000117: David Osumi-Sutherland
IAO_0000114: pending final vetting
sub property of: in neural circuit with
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

downstream in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000426: (forall (?x ?y) (iff (downstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_by ?x ?y)))) (forall (...s ?x ?y ?z) (iff (downstream_neural_circuit_path ...s ?x ?y ?z ) (and (downstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_by ?y ?z)))) (forall (?x ?y) (iff (downstream_in_neural_circuit_with ?x ?y) (exists (...s) (downstream_neural_circuit_path ?x ...s ?y))))
IAO_0000115: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
IAO_0000117: David Osumi-Sutherland
IAO_0000114: pending final vetting
sub property of: in neural circuit with
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

contained in
type: ObjectProperty
IAO_0000116: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
IAO_0000116: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
IAO_0000116: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
IAO_0000111: contained in
IAO_0000118: contained_in
range: BFO_0000004
domain: BFO_0000040
inverse of: contains
RO_0001900: RO_0001901
in_subset: eco subset
property chain axiom: RO_0001025
property chain axiom: BFO_0000050

contains
type: ObjectProperty
IAO_0000111: contains
RO_0001900: RO_0001901
in_subset: eco subset

aligned with
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000114: pending final vetting
RO_0001900: RO_0001901

RO_0002002
IAO_0000117: David Osumi-Sutherland
sub property of: mereotopologically related to

electrically_synapsed_to
type: ObjectProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000115: A relation that holds between two neurons that are electrically coupled via gap junctions.
sub property of: in neural circuit with
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

tracheates
type: ObjectProperty
IAO_0000115: The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
IAO_0000117: David Osumi-Sutherland
sub property of: contained in

innervated_by
type: ObjectProperty
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
IAO_0000117: David Osumi-Sutherland
inverse of: innervates

has synaptic terminal of
type: ObjectProperty
IAO_0000117: David Osumi-Sutherland
inverse of: has synaptic terminal in
sub property of: overlaps

bounding layer of
type: ObjectProperty
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
IAO_0000117: David Osumi-Sutherland
IAO_0000115: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
range: BFO_0000040
sub property of: BFO_0000050
in_subset: eco subset
domain: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002124

coincident with
type: ObjectProperty
IAO_0000115: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: David Osumi-Sutherland
sub property of: mereotopologically related to
in_subset: eco subset
domain: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001199
range: Class
  intersection of: BFO_0000002
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001199

cell expresses
type: ObjectProperty
description: x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y
IAO_0000115: A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
IAO_0000117: David Osumi-Sutherland
domain: cell
sub property of: expresses

regulates in other organism
type: ObjectProperty
IAO_0000115: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
IAO_0000117: David Osumi-Sutherland
range: BFO_0000015
domain: BFO_0000015
sub property of: causally upstream of or within

regulates transport of
type: ObjectProperty
IAO_0000115: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
property chain axiom: regulates
property chain axiom: transports or maintains localization of

Axiom
annotated target: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
has db xref: GOC:dos
annotated property: IAO_0000115
annotated source: regulates transport of

RO_0002082
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset

encompasses
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
IAO_0000118: di
sub property of: RO_0002088
inverse of: RO_0002092

RO_0002090
IAO_0000117: David Osumi-Sutherland
is direct form of: BFO_0000063
in_subset: eco subset
property chain axiom: RO_0002230
property chain axiom: RO_0002224

has soma location
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a neuron and an anatomical structure that its soma is part of.
domain: neuron
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: overlaps
property chain axiom: BFO_0000050

fasciculates with
type: ObjectProperty
IAO_0000426: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
IAO_0000117: David Osumi-Sutherland
IAO_0000118: fasciculates with
IAO_0000115: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
range: neuron projection bundle
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: overlaps
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
domain: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron

axon synapses in
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a neuron and some structure its axon forms (chemical) synapses in.
domain: neuron
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: has presynaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: BFO_0000050

synapsed by
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
IAO_0000114: pending final vetting
sub property of: upstream in neural circuit with
RO_0001900: RO_0001901
inverse of: synapsed to
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
range: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron

has plasma membrane part
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
IAO_0000117: Alexander Diehl
IAO_0000117: Lindsay Cowell
IAO_0000117: Chris Mungall
IAO_0000112: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
IAO_0000115: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
sub property of: BFO_0000051
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19243617

synapsed_via_type_Ib_bouton_to
type: ObjectProperty
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
IAO_0000117: David Osumi-Sutherland
IAO_0000424: BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
IAO_0000117: Marta Costa
comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
inverse of: synapsed_by_via_type_Ib_bouton
sub property of: synapsed to
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_via_type_Is_bouton_to
type: ObjectProperty
IAO_0000117: Marta Costa
IAO_0000117: David Osumi-Sutherland
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
inverse of: synapsed_by_via_type_Is_bouton
sub property of: synapsed to
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_via_type_II_bouton_to
type: ObjectProperty
IAO_0000424: BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
IAO_0000117: Marta Costa
IAO_0000117: David Osumi-Sutherland
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
inverse of: synapsed_by_via_type_II_bouton
sub property of: synapsed to

synapsed_by_via_type_II_bouton
type: ObjectProperty
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
IAO_0000117: Marta Costa
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: synapsed by
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_by_via_type_Ib_bouton
type: ObjectProperty
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
IAO_0000117: David Osumi-Sutherland
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
IAO_0000117: Marta Costa
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: synapsed by
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has postsynaptic terminal in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
IAO_0000118: synapsed in
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
inverse of: axon synapses in
sub property of: has synaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: BFO_0000050
domain: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron

releases neurotransmitter
type: ObjectProperty
IAO_0000118: has neurotransmitter
IAO_0000114: pending final vetting
sub property of: topObjectProperty

synapsed_by_via_type_Is_bouton
type: ObjectProperty
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
IAO_0000117: Marta Costa
IAO_0000117: David Osumi-Sutherland
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: synapsed by
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has presynaptic terminal in
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000118: synapses in
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: has synaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: BFO_0000050
domain: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron

synapsed_via_type_III_bouton_to
type: ObjectProperty
IAO_0000115: A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
IAO_0000424: BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
comment: Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
RO_0001900: RO_0001901
inverse of: synapsed_by_via_type_III_bouton
sub property of: synapsed to
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_by_via_type_III_bouton
type: ObjectProperty
IAO_0000115: Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
IAO_0000424: BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO_0001900: RO_0001901
sub property of: synapsed by
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed to
type: ObjectProperty
comment: N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
IAO_0000115: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000114: pending final vetting
sub property of: downstream in neural circuit with
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
domain: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron

dendrite synapsed in
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
domain: neuron
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: has postsynaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: BFO_0000050

has synaptic terminal in
type: ObjectProperty
IAO_0000115: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
IAO_0000118: has synapse in
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
IAO_0000117: David Osumi-Sutherland
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: overlaps
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
domain: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron
property chain axiom: BFO_0000050

overlaps
type: ObjectProperty
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
IAO_0000115: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: mereotopologically related to
in_subset: eco subset
property chain axiom: BFO_0000051
property chain axiom: BFO_0000050

Axiom
RO_0002582: true
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: BFO_0000051
annotated target: BFO_0000050

has fasciculating neuron projection
type: ObjectProperty
IAO_0000426: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
IAO_0000117: David Osumi-Sutherland
IAO_0000115: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
IAO_0000118: has fasciculating component
domain: neuron projection bundle
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
inverse of: fasciculates with
sub property of: overlaps
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
range: Class
  union of: neuron
  union of: Restriction
    on property: BFO_0000050
    some values from: neuron

innervates
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
domain: neuron projection bundle
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
sub property of: topObjectProperty
property chain axiom: BFO_0000050

continuous with
type: ObjectProperty
IAO_0000115: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: David Osumi-Sutherland
IAO_0000118: connected to
IAO_0000232: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
range: BFO_0000004
domain: BFO_0000004
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: mereotopologically related to

Axiom
annotated target: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
source: RO:cjm
annotated property: IAO_0000232
annotated source: continuous with

partially overlaps
type: ObjectProperty
IAO_0000426: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
IAO_0000118: proper overlaps
IAO_0000116: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
IAO_0000115: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: overlaps
in_subset: eco subset

derived by descent from
type: ObjectProperty
type: TransitiveProperty
IAO_0000118: ancestral_stucture_of
IAO_0000115: d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
IAO_0000118: evolutionarily_descended_from
IAO_0000114: pending final vetting
inverse of: has derived by descendant
sub property of: evolutionarily related to

has derived by descendant
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: pending final vetting
sub property of: evolutionarily related to

shares ancestor with
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
comment: VBO calls this homologous_to
IAO_0000115: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
IAO_0000232: Consider obsoleting and merging with child relation, 'in homology relationship with'
IAO_0000114: pending final vetting
sub property of: evolutionarily related to
property chain axiom: derived by descent from
property chain axiom: has derived by descendant

serially homologous to
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
IAO_0000114: pending final vetting
sub property of: evolutionarily related to

only in taxon
type: ObjectProperty
IAO_0000115: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
IAO_0000116: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
IAO_0000117: Chris Mungall
IAO_0000112: lactation SubClassOf 'only in taxon' some 'Mammalia'
IAO_0000114: pending final vetting
sub property of: in taxon
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
comment: Connects a biological entity to its taxon of origin.
IAO_0000117: Jennifer Deegan
IAO_0000115: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
IAO_0000117: Chris Mungall
range: BFO_0000004
IAO_0000114: pending final vetting
sub property of: evolutionarily related to
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
property chain axiom: has prototype
property chain axiom: develops from part of
property chain axiom: BFO_0000051
property chain axiom: has developmental contribution from
property chain axiom: expressed in
property chain axiom: BFO_0000050
property chain axiom: develops from
property chain axiom: capable of
property chain axiom: actively participates in

spatially disjoint from
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
IAO_0000115: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: mereotopologically related to
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

connected to
type: ObjectProperty
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
IAO_0000115: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
sub property of: mereotopologically related to
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
domain: Restriction
  on property: BFO_0000050
  some values from: system
property chain axiom:
  inverse of: connects
property chain axiom: connects
range: Restriction
  on property: BFO_0000050
  some values from: system

connects
type: ObjectProperty
IAO_0000112: The M8 connects Glasgow and Edinburgh
IAO_0000115: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
domain: BFO_0000004
sub property of: mereotopologically related to
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
range: Restriction
  on property: BFO_0000050
  some values from: system

attached to part of
type: ObjectProperty
IAO_0000115: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
sub property of: mereotopologically related to
property chain axiom: attached to
property chain axiom: BFO_0000050

Axiom
RO_0002582: true
annotated source: attached to part of
annotated property: propertyChainAxiom
annotated target: attached to
annotated target: BFO_0000050

supplies
type: ObjectProperty
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
IAO_0000115: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
sub property of: connected to
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

drains
type: ObjectProperty
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
IAO_0000115: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
sub property of: connected to
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
IAO_0000115: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
sub property of: BFO_0000051
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
in_subset: eco subset

has phenotype
type: ObjectProperty
IAO_0000115: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
IAO_0000117: Chris Mungall
domain: BFO_0000002
IAO_0000114: pending final vetting
in_subset: eco subset
sub property of: topObjectProperty

phenotype of
type: ObjectProperty
type: FunctionalProperty
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
inverse of: has phenotype
in_subset: eco subset
sub property of: topObjectProperty

develops from
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000117: Melissa Haendel
IAO_0000117: David Osumi-Sutherland
comment: This is the transitive form of the develops from relation
IAO_0000117: Terry Meehan
IAO_0000115: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
range: BFO_0000004
domain: BFO_0000004
IAO_0000114: pending final vetting
sub property of: developmentally preceded by

develops into
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
IAO_0000114: pending final vetting
inverse of: develops from
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into

gene product of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
IAO_0000116: We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
range: BFO_0000002
domain: BFO_0000004
IAO_0000114: pending final vetting
sub property of: genomically related to
property chain axiom: ribosomal translation of
property chain axiom: transcribed from

has gene product
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: every HOTAIR lncRNA is the gene product of some HOXC gene
IAO_0000115: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
IAO_0000112: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
domain: BFO_0000002
range: BFO_0000004
IAO_0000114: pending final vetting
inverse of: gene product of
sub property of: genomically related to
property chain axiom: transcribed to
property chain axiom: ribosomally translates to

expressed in
type: ObjectProperty
IAO_0000115: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
IAO_0000112: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
IAO_0000117: Chris Mungall
domain: BFO_0000002
range: BFO_0000004
IAO_0000114: pending final vetting
sub property of: genomically related to
property chain axiom: BFO_0000050

directly develops from
type: ObjectProperty
IAO_0000117: David Osumi-Sutherland
comment: TODO - add child relations from DOS
IAO_0000117: has developmental precursor
IAO_0000115: Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y
IAO_0000117: Chris Mungall
IAO_0000119: FBbt
IAO_0000114: pending final vetting
sub property of: develops from
is direct form of: develops from
range: Class
  union of: multicellular anatomical structure
  union of: cell
domain: Class
  union of: multicellular anatomical structure
  union of: cell

directly develops into
type: ObjectProperty
IAO_0000118: developmental precursor of
IAO_0000114: pending final vetting
sub property of: develops into
inverse of: directly develops from

regulates
type: ObjectProperty
IAO_0000600: false
IAO_0000115: x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
IAO_0000119: GO
IAO_0000117: Tanya Berardini
IAO_0000232: Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process.
OBO foundry unique label: regulates (processual)
IAO_0000117: Chris Mungall
IAO_0000117: David Hill
IAO_0000116: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
range: BFO_0000015
domain: BFO_0000015
IAO_0000114: pending final vetting
sub property of: causally upstream of or within
property chain axiom: BFO_0000050
property chain axiom: RO_0002230
property chain axiom: directly regulates

negatively regulates
type: ObjectProperty
OBO foundry unique label: negatively regulates (process to process)
IAO_0000115: x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
sub property of: regulates
property chain axiom: RO_0002230

positively regulates
type: ObjectProperty
OBO foundry unique label: positively regulates (process to process)
IAO_0000115: x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
sub property of: regulates
property chain axiom: RO_0002230

has prototype
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000116: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
IAO_0000116: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
IAO_0000112: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
IAO_0000115: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
IAO_0000112: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
IAO_0000114: pending final vetting

capable of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000424: RO_0000053 some (RO_0000054 only ?Y)
IAO_0000118: has function realized in
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
IAO_0000115: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
domain: BFO_0000004
range: BFO_0000015
IAO_0000114: pending final vetting
sub property of: functionally related to
sub property of: causal relation between material entity and a process
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
property chain axiom: has prototype
property chain axiom: actively participates in

capable of part of
type: ObjectProperty
IAO_0000115: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000424: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
IAO_0000118: has function in
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: capable of
property chain axiom: BFO_0000050

Axiom
RO_0002582: true
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: BFO_0000050

actively participates in
type: ObjectProperty
IAO_0000118: agent in
IAO_0000117: Chris Mungall
IAO_0000115: x actively participates in y if and only if x participates in y and x realizes some active role
IAO_0000114: pending final vetting
sub property of: RO_0000056
inverse of: has active participant

has active participant
type: ObjectProperty
IAO_0000118: has agent
IAO_0000115: x has participant y if and only if x realizes some active role that inheres in y
IAO_0000116: This may be obsoleted and replaced by the original 'has agent' relation
IAO_0000117: Chris Mungall
IAO_0000112: 'heart development' has active participant some Shh protein
IAO_0000114: pending final vetting
sub property of: RO_0000057
in_subset: eco subset

surrounded by
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: adjacent to

adjacent to
type: ObjectProperty
IAO_0000115: x adjacent to y if and only if x and y share a boundary
IAO_0000117: Chris Mungall
IAO_0000116: This relation acts as a join point with BSPO
range: BFO_0000004
domain: BFO_0000004
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
sub property of: spatially disjoint from

surrounds
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
RO_0001900: RO_0001901
inverse of: surrounded by
sub property of: adjacent to

RO_0002222
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
in_subset: eco subset

RO_0002223
IAO_0000117: Chris Mungall
sub property of: BFO_0000050
in_subset: eco subset

RO_0002224
IAO_0000117: Chris Mungall
sub property of: BFO_0000051
in_subset: eco subset

develops from part of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
IAO_0000114: pending final vetting
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: BFO_0000050

develops in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000119: Jonathan Bard, EHDAA2
IAO_0000115: x develops_in y if x is located in y whilst x is developing
IAO_0000119: EHDAA2
domain: anatomical structure
IAO_0000114: pending final vetting
sub property of: developmentally preceded by
property chain axiom: directly develops from
property chain axiom: RO_0001025

RO_0002229
IAO_0000117: Chris Mungall
sub property of: BFO_0000050
in_subset: eco subset

RO_0002230
IAO_0000117: Chris Mungall
sub property of: BFO_0000051
in_subset: eco subset

has start location
type: ObjectProperty
IAO_0000115: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
IAO_0000118: starts with process that occurs in
IAO_0000117: Chris Mungall
range: BFO_0000004
domain: BFO_0000015
IAO_0000114: pending final vetting
sub property of: has part that occurs in
in_subset: eco subset
property chain axiom: RO_0002224
property chain axiom: BFO_0000066

has end location
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000118: ends with process that occurs in
IAO_0000115: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
range: BFO_0000004
domain: BFO_0000015
IAO_0000114: pending final vetting
sub property of: has part that occurs in
in_subset: eco subset
property chain axiom: RO_0002230
property chain axiom: BFO_0000066

has input
type: ObjectProperty
IAO_0000115: p has input c if either: p has direct input c or p has indirect input c. See subrelations for definitions.
IAO_0000118: consumes
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
sub property of: RO_0000057
in_subset: eco subset
property chain axiom: RO_0002224

has output
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000118: produces
IAO_0000115: p has direct input c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of c.
IAO_0000114: pending final vetting
sub property of: RO_0000057
in_subset: eco subset
property chain axiom: RO_0002230

has developmental contribution from
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000115: x has developmental contribution from y iff x has some part z such that z develops from y
range: anatomical structure
domain: anatomical structure
IAO_0000114: pending final vetting
sub property of: developmentally preceded by
property chain axiom: BFO_0000051
property chain axiom: develops from

developmentally contributes to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
inverse of: has developmental contribution from
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: BFO_0000050

developmentally induced by
type: ObjectProperty
IAO_0000232: We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
IAO_0000119: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
IAO_0000118: induced by
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
IAO_0000119: GO:0001759
IAO_0000117: Melissa Haendel
domain: anatomical structure
range: anatomical structure
IAO_0000114: pending final vetting
sub property of: developmentally preceded by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

developmentally induces
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Inverse of developmentally induced by
IAO_0000114: pending final vetting
inverse of: developmentally induced by
sub property of: developmentally succeeded by
sub property of: has potential to developmentally induce

developmentally preceded by
type: ObjectProperty
IAO_0000116: false
IAO_0000117: Chris Mungall
IAO_0000115: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
IAO_0000114: pending final vetting
sub property of: developmentally related to

developmentally replaces
type: ObjectProperty
IAO_0000116: This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
IAO_0000117: Chris Mungall
IAO_0000115: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
IAO_0000118: replaces
IAO_0000114: pending final vetting
sub property of: developmentally preceded by

developmentally succeeded by
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Inverse of developmentally preceded by
IAO_0000114: pending final vetting
inverse of: developmentally preceded by
sub property of: has developmental potential involving

part of developmental precursor of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
IAO_0000114: pending final vetting
sub property of: developmentally succeeded by
property chain axiom: BFO_0000050
property chain axiom: directly develops into

ubiquitously expressed in
type: ObjectProperty
IAO_0000116: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
IAO_0000115: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
sub property of: expressed in

expresses
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Inverse of 'expressed in'
IAO_0000114: pending final vetting
inverse of: expressed in
sub property of: genomically related to

ubiquitously expresses
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: inverse of ubiquiotously expressed in
IAO_0000114: pending final vetting
inverse of: ubiquitously expressed in
sub property of: expresses

results in developmental progression of
type: ObjectProperty
shorthand: results_in_developmental_progression_of
IAO_0000117: Chris Mungall
IAO_0000115: p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
IAO_0000116: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
range: anatomical structure
domain: biological_process
IAO_0000114: pending final vetting
sub property of: developmentally related to

results in development of
type: ObjectProperty
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
shorthand: results_in_development_of
IAO_0000117: Chris Mungall
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000115: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
IAO_0000114: pending final vetting
sub property of: RO_0000057
sub property of: results in developmental progression of

results in formation of
type: ObjectProperty
shorthand: results_in_formation_of
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
IAO_0000112: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
IAO_0000112: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
IAO_0000114: pending final vetting
sub property of: has output
sub property of: results in developmental progression of

results in morphogenesis of
type: ObjectProperty
shorthand: results_in_morphogenesis_of
IAO_0000112: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
IAO_0000115: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
IAO_0000119: GOC:mtg_berkeley_2013
IAO_0000117: Chris Mungall
IAO_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: pending final vetting
sub property of: RO_0000057
sub property of: results in developmental progression of

results in maturation of
type: ObjectProperty
shorthand: results_in_maturation_of
IAO_0000117: Chris Mungall
IAO_0000112: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
IAO_0000115: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
IAO_0000119: GOC:mtg_berkeley_2013
IAO_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: pending final vetting
sub property of: RO_0000057
sub property of: results in developmental progression of

results in disappearance of
type: ObjectProperty
shorthand: results_in_disappearance_of
IAO_0000112: foramen ovale closure SubClassOf results in disappearance of foramen ovale
IAO_0000232: May be merged into parent relation
IAO_0000117: Chris Mungall
IAO_0000114: pending final vetting
sub property of: results in ending of

results in developmental regression of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: May be merged into parent relation
IAO_0000112: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
IAO_0000114: pending final vetting
sub property of: results in ending of

has habitat
type: ObjectProperty
IAO_0000112: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'marine environment' (ENVO_00000569) -- http://eol.org/pages/1795/overview
IAO_0000115: x 'has habitat' y if and only if: x is an organism, y is a habitat, and x is specially adapted (either naturally or via artifical selection) to living in y. Here 'living in' encompasses the majority of the animal's lifespan.
IAO_0000117: Chris Mungall
IAO_0000118: adapted for living in
domain: material anatomical entity
range: environmental system
IAO_0000114: requires discussion
sub property of: ecologically related to
in_subset: eco subset

evolutionary variant of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: evolutionarily related to

transports or maintains localization of
type: ObjectProperty
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c
IAO_0000118: regulates location of
IAO_0000118: transports
IAO_0000117: Chris Mungall
sub property of: RO_0000057
sub property of: related via localization to
property chain axiom: BFO_0000051

inheres in part of
type: ObjectProperty
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
IAO_0000117: Chris Mungall
IAO_0000115: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
RO_0001900: RO_0001901
sub property of: depends on
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
property chain axiom: RO_0000052
property chain axiom: BFO_0000050

Axiom
RO_0002582: true
annotated source: inheres in part of
annotated property: propertyChainAxiom
annotated target: RO_0000052
annotated target: BFO_0000050

results in acquisition of features of
type: ObjectProperty
shorthand: results_in_acquisition_of_features_of
IAO_0000115: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
IAO_0000112: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
IAO_0000119: GOC:mtg_berkeley_2013
IAO_0000117: Chris Mungall
range: cell
sub property of: RO_0000057
sub property of: results in developmental progression of

evolutionarily related to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: A relationship that holds via some environmental process
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.

ecologically related to
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
IAO_0000115: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000117: Chris Mungall
in_subset: eco subset

confers advantage in
type: ObjectProperty
IAO_0000116: An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
IAO_0000117: Chris Mungall
IAO_0000118: adapted for
sub property of: ecologically related to
in_subset: eco subset

mereotopologically related to
type: ObjectProperty
IAO_0000115: A mereological relationship or a topological relationship
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
IAO_0000115: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

colocalizes with
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
IAO_0000112: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
creator: Gene Ontology Consortium
IAO_0000119: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
range: BFO_0000040
domain: BFO_0000040
sub property of: mereotopologically related to

contributes to
type: ObjectProperty
IAO_0000116: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
IAO_0000112: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
IAO_0000112: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
IAO_0000112: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
IAO_0000119: http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
IAO_0000117: Chris Mungall
sub property of: capable of part of
sub property of: part of structure that is capable of

enables
type: ObjectProperty
IAO_0000232: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
IAO_0000118: has
IAO_0000118: catalyzes
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
IAO_0000118: executes
IAO_0000117: Chris Mungall
sub property of: capable of

Axiom
contributor: http://www.arabidopsis.org/
annotated target: enables
annotated source: enables
annotated property: label

functionally related to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
IAO_0000118: false
IAO_0000117: Chris Mungall
IAO_0000115: this relation holds between c and p when c is part of some c', and c' is capable of p.
sub property of: functionally related to
property chain axiom: BFO_0000050
property chain axiom: capable of

Axiom
is a defining property chain axiom: true
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: BFO_0000050
annotated target: capable of

genomically related to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
IAO_0000115: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
range: BFO_0000002
domain: BFO_0000002

involved in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000118: actively involved in
IAO_0000118: enables part of
IAO_0000115: c involved_in p if and only if c enables some process p', and p' is part of p
sub property of: involved in or regulates
property chain axiom: enables
property chain axiom: BFO_0000050

regulates levels of
type: ObjectProperty
OBO foundry unique label: regulates levels of (process to entity)
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
IAO_0000115: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: Chris Mungall
sub property of: functionally related to

enabled by
type: ObjectProperty
IAO_0000115: inverse of enables
IAO_0000117: Chris Mungall
inverse of: enables
sub property of: functionally related to
sub property of:
  inverse of: capable of

regulated by
type: ObjectProperty
OBO foundry unique label: regulated by (processual)
IAO_0000117: Chris Mungall
IAO_0000115: inverse of regulates
range: BFO_0000015
domain: BFO_0000015
inverse of: regulates
sub property of: causally downstream of or within

negatively regulated by
type: ObjectProperty
IAO_0000117: Chris Mungall
inverse of: negatively regulates
sub property of: regulated by

positively regulated by
type: ObjectProperty
IAO_0000117: Chris Mungall
inverse of: positively regulates
sub property of: regulated by

related via localization to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: A relationship that holds via some process of localization
range: BFO_0000002
domain: BFO_0000015

has target start location
type: ObjectProperty
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
IAO_0000117: Chris Mungall
sub property of: results in transport to from or in
property chain axiom: BFO_0000050

has target end location
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
sub property of: results in transport to from or in
property chain axiom: BFO_0000050

imports
type: ObjectProperty
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
IAO_0000117: Chris Mungall
sub property of: transports or maintains localization of
property chain axiom: BFO_0000051

results in transport along
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
sub property of: related via localization to

results in transport across
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
sub property of: results in transport to from or in

results in growth of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: 'pollen tube growth' results_in growth_of some 'pollen tube'
sub property of: RO_0000057
sub property of: results in developmental progression of

results in transport to from or in
type: ObjectProperty
IAO_0000112: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
IAO_0000117: Chris Mungall
sub property of: related via localization to

exports
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: transports or maintains localization of
property chain axiom: BFO_0000051

results in commitment to
type: ObjectProperty
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate
IAO_0000112: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
IAO_0000115: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
IAO_0000117: Chris Mungall
range: cell
sub property of: results in developmental progression of

results in determination of
type: ObjectProperty
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate
IAO_0000115: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
IAO_0000117: Chris Mungall
range: cell
sub property of: results in developmental progression of

input of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: RO_0000056
inverse of: has input
sub property of: functionally related to
in_subset: eco subset

output of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: RO_0000056
inverse of: has output
sub property of: functionally related to
in_subset: eco subset

formed as result of
type: ObjectProperty
IAO_0000117: Chris Mungall
inverse of: results in formation of
sub property of: output of

results in structural organization of
type: ObjectProperty
IAO_0000115: A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
IAO_0000117: Chris Mungall
sub property of: RO_0000057
sub property of: results in developmental progression of

results in specification of
type: ObjectProperty
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml#fate
IAO_0000117: Chris Mungall
IAO_0000115: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
range: cell
sub property of: results in developmental progression of

results in developmental induction of
type: ObjectProperty
IAO_0000115: p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
IAO_0000117: Chris Mungall
sub property of: results in developmental progression of

has dendrite location
type: ObjectProperty
source: http://neurolex.org/wiki/Property:DendriteLocation
IAO_0000117: Chris Mungall
sub property of: overlaps

attached to
type: ObjectProperty
type: SymmetricProperty
IAO_0000117: Chris Mungall
IAO_0000115: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
sub property of: connected to
sub property of: attached to part of
in_subset: eco subset

has muscle origin
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Insertion_(anatomy)
IAO_0000115: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
sub property of: attached to
sub property of: biomechanically related to

has muscle insertion
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000119: Wikipedia:Insertion_(anatomy)
IAO_0000115: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
sub property of: attached to
sub property of: biomechanically related to

has fused element
type: ObjectProperty
IAO_0000112: false
IAO_0000117: Chris Mungall
comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.
IAO_0000115: x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
IAO_0000114: requires discussion
sub property of: evolutionarily related to
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

in branching relationship with
type: ObjectProperty
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
IAO_0000117: Chris Mungall
range: BFO_0000040
domain: BFO_0000040
sub property of: BFO_0000050
IAO_0000114: requires discussion
sub property of: mereotopologically related to

tributary of
type: ObjectProperty
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
IAO_0000112: inferior epigastric vein tributary_of external iliac vein
IAO_0000118: tributary channel of
IAO_0000119: http://www.medindia.net/glossary/venous_tributary.htm
IAO_0000119: http://en.wikipedia.org/wiki/Tributary
IAO_0000115: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
IAO_0000118: drains to
IAO_0000112: Deschutes River tributary_of Columbia River
IAO_0000118: drains into
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: in branching relationship with
in_subset: eco subset

Axiom
annotated target: inferior epigastric vein tributary_of external iliac vein
source: FMA
annotated property: IAO_0000112
annotated source: tributary of

Axiom
annotated target: drains to
source: drainsTo
annotated property: IAO_0000118
annotated source: tributary of

Axiom
source: GAZ
annotated target: Deschutes River tributary_of Columbia River
annotated property: IAO_0000112
annotated source: tributary of

distributary of
type: ObjectProperty
IAO_0000112: Deschutes River distributary_of Little Lava Lake
IAO_0000118: distributary channel of
IAO_0000115: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
IAO_0000119: http://en.wikipedia.org/wiki/Distributary
IAO_0000117: Chris Mungall
IAO_0000118: branch of
IAO_0000114: requires discussion
sub property of: in branching relationship with
in_subset: eco subset

Axiom
annotated target: Deschutes River distributary_of Little Lava Lake
source: GAZ
annotated property: IAO_0000112
annotated source: distributary of

anabranch of
type: ObjectProperty
IAO_0000118: anastomoses with
IAO_0000115: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: distributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
in_subset: eco subset
sub property of:
  inverse of: tributary of

spatially coextensive with
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x spatially_coextensive_with y if and inly if x and y have the same location
IAO_0000232: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
IAO_0000112: A lump of clay and a statue
sub property of: overlaps
property chain axiom: RO_0001025
property chain axiom:
  inverse of: RO_0001025

branching part of
type: ObjectProperty
IAO_0000115: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
IAO_0000117: Chris Mungall
sub property of: BFO_0000050
IAO_0000114: requires discussion
sub property of: in branching relationship with
in_subset: eco subset
range: Restriction
  on property: RO_0000053
  some values from: branched
property chain axiom: distributary of
property chain axiom: main stem of

main stem of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
IAO_0000114: requires discussion
sub property of: in branching relationship with
in_subset: eco subset

proper distributary of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
IAO_0000114: requires discussion
sub property of: distributary of
in_subset: eco subset

proper tributary of
type: ObjectProperty
IAO_0000115: x proper_tributary_of y iff x tributary_of y and x does not originate from y
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: tributary of
in_subset: eco subset

has developmental potential involving
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000114: requires discussion
sub property of: developmentally related to

has potential to developmentally contribute to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000114: requires discussion
sub property of: has developmental potential involving

has potential to developmentally induce
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
IAO_0000114: requires discussion
sub property of: has developmental potential involving

has potential to develop into
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000114: requires discussion
sub property of: has developmental potential involving

has potential to directly develop into
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000114: requires discussion
sub property of: has potential to develop into

has direct input
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000232: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
IAO_0000112: 'protein catabolic process' SubClassOf has_direct_input some protein
IAO_0000118: directly consumes
IAO_0000114: requires discussion
sub property of: has input
property chain axiom: RO_0002224

obsolete has indirect input
type: ObjectProperty
deprecated: true
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion

obsolete has direct output
type: ObjectProperty
deprecated: true
IAO_0000118: directly produces
IAO_0000117: Chris Mungall
IAO_0000112: translation SubClassOf has_direct_output some protein
IAO_0000115: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
IAO_0000114: requires discussion

obsolete has indirect output
type: ObjectProperty
deprecated: true
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: has output
property chain axiom: causally upstream of
property chain axiom: obsolete has direct output

causally downstream of
type: ObjectProperty
IAO_0000115: inverse of upstream of
IAO_0000117: Chris Mungall
sub property of: BFO_0000062
IAO_0000114: requires discussion
inverse of: causally upstream of
sub property of: causally downstream of or within

immediately causally downstream of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: RO_0002087
sub property of: causally downstream of
inverse of: immediately causally upstream of

directly activates
type: ObjectProperty
IAO_0000118: directly positively regulates
OBO foundry unique label: directly activates (process to process)
IAO_0000115: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: positively regulates
sub property of: immediately causally upstream of
sub property of: directly regulates

indirectly activates
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000115: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
IAO_0000118: indirectly positively regulates
IAO_0000114: requires discussion
sub property of: positively regulates
is indirect form of: positively regulates
property chain axiom: directly activates

directly inhibits
type: ObjectProperty
IAO_0000118: directly negatively regulates
IAO_0000117: Chris Mungall
OBO foundry unique label: directly inhibits (process to process)
IAO_0000114: requires discussion
sub property of: negatively regulates
sub property of: immediately causally upstream of
sub property of: directly regulates

indirectly inhibits
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000118: indirectly negatively regulates
IAO_0000114: requires discussion
sub property of: negatively regulates
is indirect form of: negatively regulates
property chain axiom: directly inhibits

causally related to
type: ObjectProperty
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
IAO_0000117: Chris Mungall
IAO_0000115: This relation groups causal relations between material entities and causal relations between processes
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000114: requires discussion

causally upstream of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
sub property of: BFO_0000063
IAO_0000114: requires discussion
sub property of: causally upstream of or within

immediately causally upstream of
type: ObjectProperty
IAO_0000115: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion
sub property of: RO_0002090
sub property of: causally upstream of
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
OBO foundry unique label: directly provides input for (process to process)
IAO_0000115: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
IAO_0000117: Chris Mungall
IAO_0000116: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
IAO_0000114: requires discussion
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: obsolete has direct output
property chain axiom: has direct input

transitively provides input for
type: ObjectProperty
type: TransitiveProperty
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
OBO foundry unique label: transitively provides input for (process to process)
IAO_0000117: Chris Mungall
IAO_0000115: transitive form of directly_provides_input_for
range: BFO_0000015
domain: BFO_0000015
IAO_0000114: requires discussion
sub property of: causally upstream of

causally upstream of or within
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
IAO_0000118: influences (processual)
IAO_0000117: Chris Mungall
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
sub property of: causal relation between processes

differs in
type: ObjectProperty
IAO_0000116: false
comment: This is an exploratory relation
IAO_0000117: Chris Mungall

differs in attribute of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: differs in
range: Class
  union of: BFO_0000004
  union of: BFO_0000015

differs in attribute
type: ObjectProperty
IAO_0000117: Chris Mungall
range: BFO_0000020
sub property of: differs in

causally downstream of or within
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
inverse of: causally upstream of or within
sub property of: causal relation between processes

involved in regulation of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: c involved in regulation of p if c is involved in some 'p' and p' regulates some p
sub property of: involved in or regulates
property chain axiom: involved in
property chain axiom: regulates
property chain axiom: enables

involved in positive regulation of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in

involved in negative regulation of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in

involved in or regulates
type: ObjectProperty
IAO_0000118: involved in or involved in regulation of
IAO_0000115: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000117: Chris Mungall
sub property of: functionally related to

enables activity in
type: ObjectProperty
IAO_0000115: c executes activity in d if and only if c enables p and p occurs_in d
IAO_0000118: executes activity in
IAO_0000117: Chris Mungall
sub property of: functionally related to
property chain axiom: enables
property chain axiom: BFO_0000066

Axiom
is a defining property chain axiom: true
annotated source: enables activity in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: BFO_0000066

contributes to morphology of
type: ObjectProperty
IAO_0000115: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
IAO_0000117: Chris Mungall
sub property of: overlaps

interacts with
type: ObjectProperty
type: SymmetricProperty
IAO_0000116: Considering relabeling as 'pairwise interacts with'
has exact synonym: in pairwise interaction with
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
IAO_0000117: Chris Mungall
IAO_0000115: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
domain: BFO_0000040
range: BFO_0000040
in_subset: eco subset

genetically interacts with
type: ObjectProperty
type: SymmetricProperty
IAO_0000116: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
IAO_0000117: Chris Mungall
sub property of: interacts with

molecularly interacts with
type: ObjectProperty
type: SymmetricProperty
IAO_0000118: molecularly binds with
IAO_0000117: Chris Mungall
IAO_0000115: An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected.
IAO_0000118: binds
sub property of: interacts with

biotically interacts with
type: ObjectProperty
type: SymmetricProperty
IAO_0000117: Chris Mungall
IAO_0000115: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000118: interacts with on organism level
range: BFO_0000040
domain: BFO_0000040
sub property of: ecologically related to
sub property of: interacts with
in_subset: eco subset

trophically interacts with
type: ObjectProperty
IAO_0000115: An interaction relationship in which the partners are related via a feeding relationship.
IAO_0000117: Chris Mungall
sub property of: participates in a biotic-biotic interaction with
in_subset: eco subset

preys on
type: ObjectProperty
IAO_0000112: Baleen whale preys on krill
IAO_0000115: An interaction relationship involving a predation process, where the subject consumes all or part of the target
IAO_0000118: is subject of predation interaction with
IAO_0000117: Chris Mungall
IAO_0000118: preys upon
sub property of: trophically interacts with
in_subset: eco subset

symbiotically interacts with
type: ObjectProperty
type: SymmetricProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
IAO_0000117: Chris Mungall
IAO_0000115: A biotic interaction in which the two organisms live together in more or less intimate association.
is symmetric relational form of process class: GO_0044403
sub property of: participates in a biotic-biotic interaction with
in_subset: eco subset
property chain axiom: partner in
property chain axiom: is symbiosis
property chain axiom:
  inverse of: partner in

Axiom
source: http://www.ncbi.nlm.nih.gov/pubmed/19278549
annotated target: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
annotated property: IAO_0000232
annotated source: symbiotically interacts with

commensually interacts with
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
IAO_0000117: Chris Mungall
is symmetric relational form of process class: GO_0085031
sub property of: symbiotically interacts with
in_subset: eco subset
property chain axiom: partner in
property chain axiom: is commensalism
property chain axiom:
  inverse of: partner in

mutualistically interacts with
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
IAO_0000117: Chris Mungall
is symmetric relational form of process class: GO_0085030
sub property of: symbiotically interacts with
in_subset: eco subset
property chain axiom: partner in
property chain axiom: is mutualism
property chain axiom:
  inverse of: partner in

interacts with via parasite-host interaction
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: This relation groups a pair of inverse relations, parasite of and parasitized by
IAO_0000117: Chris Mungall
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
is symmetric relational form of process class: GO_0072519
sub property of: symbiotically interacts with
in_subset: eco subset
property chain axiom: partner in
property chain axiom: is parasitism
property chain axiom:
  inverse of: partner in

parasite of
type: ObjectProperty
IAO_0000118: parasitizes
IAO_0000117: Chris Mungall
IAO_0000112: Pediculus humanus capitis parasite of human
is asymmetric relational form of process class: GO_0072519
sub property of: interacts with via parasite-host interaction
sub property of: has host
in_subset: eco subset
property chain axiom: subject participant in
property chain axiom: is parasitism
property chain axiom:
  inverse of: target participant in

parasitized by
type: ObjectProperty
IAO_0000118: parasitised by
IAO_0000118: has parasite
IAO_0000117: Chris Mungall
sub property of: interacts with via parasite-host interaction
inverse of: parasite of
sub property of: host of
in_subset: eco subset

participates in a abiotic-biotic interaction with
type: ObjectProperty
IAO_0000115: A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
IAO_0000112: Porifiera attaches to substrate
has related synonym: semibiotically interacts with
IAO_0000117: Chris Mungall
sub property of: biotically interacts with
in_subset: eco subset

phosphorylates
type: ObjectProperty
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is kinase activity
property chain axiom: has direct input

molecularly controls
type: ObjectProperty
IAO_0000115: Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
IAO_0000117: Chris Mungall
sub property of: molecularly interacts with
sub property of: causally influences
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by

molecularly decreases activity of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
IAO_0000118: inhibits
sub property of: molecularly controls
property chain axiom: enables
property chain axiom: directly inhibits
property chain axiom: enabled by

molecularly increases activity of
type: ObjectProperty
IAO_0000118: activates
IAO_0000117: Chris Mungall
IAO_0000115: Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b.
sub property of: molecularly controls
property chain axiom: enables
property chain axiom: directly activates
property chain axiom: enabled by

transmitted by
type: ObjectProperty
IAO_0000116: Add domain and range constraints
IAO_0000112: all dengue disease transmitted by some mosquito
IAO_0000115: A relationship that holds between a disease and organism
IAO_0000117: Chris Mungall
sub property of: ecologically related to

has symptom
type: ObjectProperty
IAO_0000115: A relation that holds between a disease or an organism and a phenotype
IAO_0000117: Chris Mungall
sub property of: has phenotype

host of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
sub property of: symbiotically interacts with
in_subset: eco subset

has host
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: symbiotically interacts with
in_subset: eco subset

pollinates
type: ObjectProperty
IAO_0000118: is subject of pollination interaction with
IAO_0000116: This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
IAO_0000117: Chris Mungall
IAO_0000112: Bees pollinate Flowers
sub property of: mutualistically interacts with
in_subset: eco subset

pollinated by
type: ObjectProperty
IAO_0000118: has polinator
IAO_0000118: is target of pollination interaction with
IAO_0000117: Chris Mungall
sub property of: mutualistically interacts with
inverse of: pollinates
in_subset: eco subset

acquires nutrients from
type: ObjectProperty
IAO_0000232: Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
IAO_0000117: Chris Mungall
sub property of: trophically interacts with
in_subset: eco subset

preyed upon by
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000118: is target of predation interaction with
IAO_0000118: has predator
sub property of: trophically interacts with
inverse of: preys on
in_subset: eco subset

is vector for
type: ObjectProperty
IAO_0000119: a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
IAO_0000112: Anopheles is a vector for Plasmodium
IAO_0000117: Chris Mungall
inverse of: has vector
sub property of: participates in a biotic-biotic interaction with
in_subset: eco subset

has vector
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: is vector for
in_subset: eco subset

partner in
type: ObjectProperty
IAO_0000232: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
IAO_0000117: Chris Mungall
sub property of: RO_0000056

subject participant in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
sub property of: partner in

target participant in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
sub property of: partner in

helper property
type: ObjectProperty
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
IAO_0000117: Chris Mungall
IAO_0000114: requires discussion

is symbiosis
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: interaction relation helper property

is commensalism
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: is symbiosis

is mutualism
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: is symbiosis

is parasitism
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: is symbiosis

provides nutrients for
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: trophically interacts with
inverse of: acquires nutrients from
in_subset: eco subset

eats
type: ObjectProperty
IAO_0000118: is subject of eating interaction with
IAO_0000117: Chris Mungall
sub property of: trophically interacts with
in_subset: eco subset

is eaten by
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000118: is target of eating interaction with
sub property of: trophically interacts with
in_subset: eco subset

is evidence for
type: ObjectProperty
IAO_0000115: A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
IAO_0000117: Chris Mungall
in_subset: eco subset

composed primarily of
type: ObjectProperty
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
IAO_0000115: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
IAO_0000117: Chris Mungall
sub property of: BFO_0000051
RO_0001900: RO_0001901
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

child nucleus of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.
IAO_0000112: ABal nucleus child nucleus of ABa nucleus (in C elegans)
IAO_0000115: c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
domain: nucleus
range: nucleus
sub property of: developmentally preceded by

child nucleus of in hermaphrodite
type: ObjectProperty
IAO_0000115: A child nucleus relationship in which the cells are part of a hermaphroditic organism
IAO_0000117: Chris Mungall
sub property of: child nucleus of

child nucleus of in male
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: A child nucleus relationship in which the cells are part of a male organism
sub property of: child nucleus of

has part that occurs in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
domain: BFO_0000003
range: BFO_0000004
in_subset: eco subset
property chain axiom: BFO_0000051
property chain axiom: BFO_0000066

Axiom
is a defining property chain axiom: true
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: BFO_0000051
annotated target: BFO_0000066

ubiquitinates
type: ObjectProperty
IAO_0000116: Axiomatization to GO to be added later
IAO_0000115: An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
IAO_0000117: Chris Mungall
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is ubiquitination
property chain axiom: has direct input

is kinase activity
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: molecular interaction relation helper property

is ubiquitination
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: molecular interaction relation helper property

receives input from
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000116: See notes for inverse relation
sub property of: connected to
inverse of: sends output to

sends output to
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000116: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
sub property of: connected to

relation between structure and stage
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
IAO_0000117: Chris Mungall
domain: BFO_0000002
range: BFO_0000003

existence starts during
type: ObjectProperty
IAO_0000115: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: Chris Mungall
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: existence starts at point
property chain axiom: BFO_0000050

existence starts with
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
sub property of: existence starts during
property chain axiom: existence starts at point
property chain axiom:
  inverse of: existence starts at point

existence overlaps
type: ObjectProperty
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
IAO_0000117: Chris Mungall
IAO_0000115: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
sub property of: relation between structure and stage

existence starts and ends during
type: ObjectProperty
IAO_0000115: x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
IAO_0000117: Chris Mungall
sub property of: existence starts during
sub property of: existence ends during

existence ends during
type: ObjectProperty
IAO_0000115: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: BFO_0000050
property chain axiom: existence ends at point

existence ends with
type: ObjectProperty
IAO_0000115: x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
IAO_0000117: Chris Mungall
sub property of: existence ends during
property chain axiom: existence ends at point
property chain axiom:
  inverse of: existence ends at point

transformation of
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000115: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
sub property of: BFO_0000062
sub property of: develops from

immediate transformation of
type: ObjectProperty
IAO_0000115: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
IAO_0000117: Chris Mungall
sub property of: RO_0002087
sub property of: directly develops from
is direct form of: transformation of
sub property of: transformation of

existence starts during or after
type: ObjectProperty
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
IAO_0000115: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: Chris Mungall
sub property of: relation between structure and stage
property chain axiom: BFO_0000050
property chain axiom: developmentally preceded by
property chain axiom: existence starts at point
property chain axiom: BFO_0000062
property chain axiom:
  inverse of: existence starts at point
property chain axiom: RO_0002082

existence ends during or before
type: ObjectProperty
IAO_0000117: Chris Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
IAO_0000115: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
sub property of: relation between structure and stage
property chain axiom: developmentally succeeded by
property chain axiom: existence ends at point
property chain axiom: BFO_0000063
property chain axiom:
  inverse of: existence ends at point
property chain axiom: BFO_0000050
property chain axiom: RO_0002082

causal relation between processes
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000119: https://docs.google.com/document/d/1WxocTXZaGVhEV1n7NB86pCF3SUcBJh8bq4vQrVCkjSU/edit#
IAO_0000115: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
domain: BFO_0000003
range: BFO_0000003
sub property of: causally related to

depends on
type: ObjectProperty
IAO_0000117: Chris Mungall

towards
type: ObjectProperty
IAO_0000116: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
IAO_0000117: Chris Mungall
IAO_0000115: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
sub property of: depends on
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
IAO_0000115: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
IAO_0000118: has intermediate product
sub property of: RO_0000057
in_subset: eco subset

causal relation between material entities
type: ObjectProperty
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: Chris Mungall
range: BFO_0000040
domain: BFO_0000040
sub property of: causally related to

determined by
type: ObjectProperty
creator: Pier Buttigieg
OBO foundry unique label: determined by (system to material entity)
IAO_0000112: A coral reef environment is determined by a particular coral reef
IAO_0000117: Chris Mungall
creator: Chris Mungall
IAO_0000116: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
IAO_0000115: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
range: BFO_0000040
sub property of: BFO_0000050
sub property of: determined by part of
sub property of: causally influenced by
domain: system
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/24330602

determines
type: ObjectProperty
OBO foundry unique label: determines (material entity to system)
IAO_0000117: Chris Mungall
inverse of: determined by
sub property of: causally influences
in_subset: eco subset

determined by part of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
range: BFO_0000040
sub property of: overlaps
sub property of: causal relation between material entities
domain: system
in_subset: eco subset
property chain axiom: determined by
property chain axiom: BFO_0000050

Axiom
RO_0002582: true
annotated source: determined by part of
annotated property: propertyChainAxiom
annotated target: determined by
annotated target: BFO_0000050

transcribed from
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000115: x is transcribed from y if and only if x is synthesized from template y
IAO_0000117: Chris Mungall
sub property of: genomically related to

transcribed to
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000117: Chris Mungall
sub property of: genomically related to
inverse of: transcribed from

ribosomal translation of
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000115: x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
IAO_0000117: Chris Mungall
sub property of: genomically related to

ribosomally translates to
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000115: inverse of ribosomal translation of
IAO_0000117: Chris Mungall
sub property of: genomically related to

sequentially related to
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000115: A relation that holds between two entities that have the property of being sequences or having sequences.
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: Chris Mungall
IAO_0000232: The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
cites as authority: 006650.abstract
domain: sequentially ordered entity
range: sequentially ordered entity

sequentially adjacent to
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000112: Every UTR is adjacent to a CDS of the same transcript
IAO_0000112: Two consecutive DNA residues are sequentially adjacent
IAO_0000112: Two exons on a processed transcript that were previously connected by an intron are adjacent
IAO_0000117: Chris Mungall
IAO_0000115: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
cites as authority: 006650.abstract
sub property of: does not overlap sequence of

has start sequence
type: ObjectProperty
type: TransitiveProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000112: Every CDS has as a start sequence the start codon for that transcript
IAO_0000117: Chris Mungall
IAO_0000118: started by
IAO_0000115: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
cites as authority: 006650.abstract
inverse of: is start sequence of
sub property of: has subsequence

is start sequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000117: Chris Mungall
IAO_0000118: starts
IAO_0000115: inverse of has start sequence
cites as authority: 006650.abstract
sub property of: is subsequence of

has end sequence
type: ObjectProperty
type: TransitiveProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000117: Chris Mungall
IAO_0000112: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
IAO_0000118: ended by
IAO_0000115: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
cites as authority: 006650.abstract
inverse of: is end sequence of
sub property of: has subsequence

is end sequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000118: ends
IAO_0000117: Chris Mungall
IAO_0000115: inverse of has end sequence
cites as authority: 006650.abstract
sub property of: is subsequence of

is consecutive sequence of
type: ObjectProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000116: In the SO paper, this was defined as an instance-type relation
IAO_0000117: Chris Mungall
IAO_0000115: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
cites as authority: 006650.abstract
sub property of: has subsequence

is sequentially aligned with
type: ObjectProperty
type: SymmetricProperty
IAO_0000112: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
IAO_0000115: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
sub property of: sequentially related to

bounds sequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000115: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
IAO_0000112: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
cites as authority: 006650.abstract
sub property of: sequentially related to

is bound by sequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: inverse of bounds sequence of
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
sub property of: sequentially related to
inverse of: bounds sequence of

has subsequence
type: ObjectProperty
type: TransitiveProperty
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
IAO_0000117: Chris Mungall
IAO_0000118: contains
IAO_0000115: x has subsequence y iff all of the sequence parts of x are sequence parts of y
cites as authority: 006650.abstract
sub property of: BFO_0000051
sub property of: bounds sequence of
sub property of: overlaps sequence of

is subsequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000118: contained by
IAO_0000115: inverse of has subsequence
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
sub property of: BFO_0000050
sub property of: is bound by sequence of
inverse of: has subsequence
sub property of: overlaps sequence of

overlaps sequence of
type: ObjectProperty
type: SymmetricProperty
IAO_0000115: x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
sub property of: overlaps
sub property of: sequentially related to
property chain axiom: has subsequence
property chain axiom: is subsequence of

does not overlap sequence of
type: ObjectProperty
type: SymmetricProperty
IAO_0000117: Chris Mungall
IAO_0000118: disconnected from
IAO_0000115: x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
cites as authority: 006650.abstract
sub property of: sequentially related to

is upstream of sequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000115: inverse of downstream of sequence of
cites as authority: 006650.abstract
sub property of: does not overlap sequence of

is downstream of sequence of
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000115: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
cites as authority: 006650.abstract
sub property of: does not overlap sequence of

is immediately downstream of sequence of
type: ObjectProperty
IAO_0000115: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
IAO_0000112: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000117: Chris Mungall
cites as authority: 006650.abstract
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of
is direct form of: is downstream of sequence of

is immediately upstream of sequence of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
IAO_0000115: inverse of immediately downstream of
cites as authority: 006650.abstract
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of

has skeleton
type: ObjectProperty
IAO_0000115: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
IAO_0000118: has supporting framework
IAO_0000232: The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
IAO_0000117: Chris Mungall
IAO_0000112: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
sub property of: BFO_0000051

results in ending of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
sub property of: RO_0000057
sub property of: results in developmental progression of

hyperparasite of
type: ObjectProperty
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000115: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
IAO_0000117: Chris Mungall
has related synonym: hyperparasitoid of
sub property of: has host
in_subset: eco subset
property chain axiom: parasite of

hyperparasitized by
type: ObjectProperty
IAO_0000117: Chris Mungall
has related synonym: hyperparasitoidized by
sub property of: host of
inverse of: hyperparasite of
in_subset: eco subset
property chain axiom: parasitized by

allelopath of
type: ObjectProperty
IAO_0000117: Chris Mungall
see also: x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y
IAO_0000119: http://en.wikipedia.org/wiki/Allelopathy
sub property of: participates in a biotic-biotic interaction with
in_subset: eco subset

pathogen of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: has host
inverse of: has pathogen
in_subset: eco subset

has pathogen
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: host of
in_subset: eco subset

has evidence
type: ObjectProperty
comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
IAO_0000117: Chris Mungall
inverse of: is evidence for
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/25052702

causally influenced by
type: ObjectProperty
IAO_0000117: Chris Mungall
OBO foundry unique label: causally influenced by (material entity to material entity)
sub property of: causal relation between material entities

interaction relation helper property
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: helper property

molecular interaction relation helper property
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: interaction relation helper property

results in movement of
type: ObjectProperty
IAO_0000115: Holds between p and c when p is a movement or chemotaxis process and the outcome of this process is the change of location of c
IAO_0000117: Chris Mungall
sub property of: RO_0000057

Axiom
has db xref: GOC:mtg_berkeley_2013
annotated target: Holds between p and c when p is a movement or chemotaxis process and the outcome of this process is the change of location of c
annotated property: IAO_0000115
annotated source: results in movement of

causally influences
type: ObjectProperty
IAO_0000115: Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
IAO_0000117: Chris Mungall
OBO foundry unique label: causally influences (material entity to material entity)
sub property of: causal relation between material entities
inverse of: causally influenced by
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: enabled by
property chain axiom: has input

biomechanically related to
type: ObjectProperty
IAO_0000115: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: Chris Mungall
sub property of: functionally related to

has muscle antagonist
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
IAO_0000119: Wikipedia:Antagonist_(muscle)
sub property of: biomechanically related to

has branching part
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: in branching relationship with
inverse of: branching part of
in_subset: eco subset

conduit for
type: ObjectProperty
IAO_0000232: This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
IAO_0000115: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
IAO_0000119: UBERON:cjm
IAO_0000117: Chris Mungall
range: BFO_0000040
domain: BFO_0000040
sub property of: overlaps
in_subset: eco subset

lumen of
type: ObjectProperty
IAO_0000115: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
IAO_0000117: Chris Mungall
IAO_0000119: GOC:cjm
range: BFO_0000040
sub property of: BFO_0000050
in_subset: eco subset

luminal space of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
domain: BFO_0000141
sub property of: lumen of
in_subset: eco subset

has modifier
type: ObjectProperty
IAO_0000232: This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
IAO_0000117: Chris Mungall
IAO_0000115: A relation that holds between an attribute or a qualifier and another attribute.
domain: PATO_0000001
in_subset: eco subset
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

participates in a biotic-biotic interaction with
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: biotically interacts with
in_subset: eco subset

skeleton of
type: ObjectProperty
IAO_0000117: Chris Mungall
sub property of: BFO_0000050
range: anatomical structure
domain: anatomical structure
inverse of: has skeleton

directly regulates
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p
OBO foundry unique label: directly regulates (processual)
is direct form of: regulates
sub property of: regulates
sub property of: immediately causally upstream of

existence starts at point
type: ObjectProperty
IAO_0000115: x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.
sub property of: relation between structure and stage

has part structure that is capable of
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
IAO_0000115: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: BFO_0000051
property chain axiom: capable of

results in closure of
type: ObjectProperty
IAO_0000116: p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
sub property of: RO_0000057
sub property of: results in developmental progression of

results in breakdown of
type: ObjectProperty
IAO_0000115: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
sub property of: has input

results in synthesis of
type: ObjectProperty
sub property of: results in formation of

results in assembly of
type: ObjectProperty
sub property of: results in formation of
sub property of: results in organization of

results in catabolism of
type: ObjectProperty
IAO_0000115: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
sub property of: results in breakdown of

results in disassembly of
type: ObjectProperty
sub property of: results in breakdown of
sub property of: results in organization of

results in remodeling of
type: ObjectProperty
sub property of: has input
sub property of: results in organization of

results in organization of
type: ObjectProperty
IAO_0000115: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
sub property of: RO_0000057

existence ends at point
type: ObjectProperty
IAO_0000115: x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.
sub property of: relation between structure and stage

causal relation between material entity and a process
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
range: BFO_0000015
domain: BFO_0000040
sub property of: causally related to

capable of regulating
type: ObjectProperty
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000112: pyrethroid -> growth
sub property of: causal relation between material entity and a process
property chain axiom: capable of
property chain axiom: regulates

capable of negatively regulating
type: ObjectProperty
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates

capable of positively regulating
type: ObjectProperty
IAO_0000112: renin -> arteriolar smooth muscle contraction
IAO_0000115: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates

capable of inhibiting or preventing pathological process
type: ObjectProperty
IAO_0000232: The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
IAO_0000112: pazopanib -> pathological angiogenesis
IAO_0000118: treats
sub property of: capable of negatively regulating

Axiom
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
annotated target: treats
annotated property: IAO_0000118
annotated source: capable of inhibiting or preventing pathological process

capable of upregulating or causing pathological process
type: ObjectProperty
IAO_0000118: causes disease
IAO_0000112: benzene -> cancer [CHEBI]
IAO_0000115: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
sub property of: capable of positively regulating

produces
type: ObjectProperty
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
IAO_0000115: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
IAO_0000117: Melissa Haendel
domain: BFO_0000040
range: BFO_0000040
IAO_0000114: pending final vetting
inverse of: produced by
in_subset: eco subset
property chain axiom:
  inverse of: BFO_0000066
property chain axiom: has output

produced by
type: ObjectProperty
IAO_0000117: Melissa Haendel
range: BFO_0000040
domain: BFO_0000040
IAO_0000114: pending final vetting
in_subset: eco subset

represses expression of
type: ObjectProperty
IAO_0000116: Logical axioms to be added after the relevant branch of GO is MIREOTed in
IAO_0000115: Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
sub property of: molecularly decreases activity of

increases expression of
type: ObjectProperty
IAO_0000115: Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
IAO_0000116: Logical axioms to be added after the relevant branch of GO is MIREOTed in
sub property of: molecularly increases activity of

anatomical structure
type: Class
subclass of: material anatomical entity
IAO_0000412: caro.owl

material anatomical entity
type: Class
subclass of: BFO_0000040
IAO_0000412: caro.owl

immaterial anatomical entity
type: Class
subclass of: BFO_0000141

connected anatomical system
type: Class
subclass of: material anatomical entity
subclass of: system

cell part
type: Class
subclass of: anatomical structure
OBO foundry unique label: cell part (CARO)
IAO_0000412: caro.owl

multi-cell-part structure
type: Class
subclass of: anatomical structure
IAO_0000412: caro.owl

neuron projection bundle
type: Class
subclass of: multi-cell-part structure
IAO_0000412: caro.owl

multicellular anatomical structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: directly develops from
  all values from: multicellular anatomical structure
IAO_0000412: caro.owl

cell
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: directly develops from
  all values from: cell
IAO_0000412: cl.owl

neuron
type: Class
subclass of: cell
IAO_0000412: cl.owl

biome
type: Class
subclass of: environmental system

habitat
type: Class
subclass of: environmental system

environmental system
type: Class
subclass of: system

GO_0003674
subclass of: BFO_0000015
OBO foundry unique label: molecular process

GO_0004842
subclass of: Restriction
  on property: is ubiquitination
  has self: true

nucleus
type: Class
subclass of: cell part
IAO_0000412: go.owl

biological_process
type: Class
subclass of: BFO_0000015

membrane
type: Class
subclass of: cell part
IAO_0000412: go.owl

GO_0016301
subclass of: Restriction
  on property: is kinase activity
  has self: true

axon
type: Class
subclass of: neuron projection
IAO_0000412: go.owl

dendrite
type: Class
subclass of: neuron projection
IAO_0000412: go.owl

presynaptic membrane
type: Class
subclass of: membrane
subclass of: synapse part
IAO_0000412: go.owl

cell projection
type: Class
subclass of: cell part
IAO_0000412: go.owl

neuron projection
type: Class
subclass of: cell projection
IAO_0000412: go.owl

GO_0044403
subclass of: Restriction
  on property: is symbiosis
  has self: true

synapse part
type: Class
subclass of: cell part
IAO_0000412: go.owl

cell part
type: Class
subclass of: cell part
IAO_0000412: go.owl

synapse
type: Class
subclass of: cell part
IAO_0000412: go.owl

postsynaptic membrane
type: Class
subclass of: membrane
subclass of: synapse part
IAO_0000412: go.owl

GO_0072519
subclass of: Restriction
  on property: is parasitism
  has self: true

GO_0085030
subclass of: Restriction
  on property: is mutualism
  has self: true

GO_0085031
subclass of: Restriction
  on property: is commensalism
  has self: true

PATO_0000001
subclass of: BFO_0000020
OBO foundry unique label: quality (PATO)

shape
type: Class
subclass of: PATO_0000051

branched
type: Class
subclass of: branchiness

branchiness
type: Class
subclass of: shape

sequentially ordered entity
type: Class
subclass of: Restriction
  on property: has subsequence
  some values from: sequence atomic unit
IAO_0000117: Chris Mungall
IAO_0000115: Any entity that is ordered in discrete units along a linear axis.

sequence atomic unit
type: Class
subclass of: sequentially ordered entity
IAO_0000115: Any individual unit of a collection of like units arranged in a linear order
IAO_0000232: An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.
IAO_0000117: Chris Mungall

sequence bearer
type: Class
subclass of: sequentially ordered entity
IAO_0000115: Any entity that can be divided into parts such that each part is an atomical unit of a sequence
IAO_0000117: Chris Mungall
IAO_0000232: Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.

system
type: Class
subclass of: BFO_0000040
IAO_0000115: A material entity consisting of multiple components that are causally integrated.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.jbiomedsem.com/content/4/1/43
IAO_0000116: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43

RO_0001000
IAO_0000232: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
in_subset: eco subset

requires discussion
IAO_0000114: pending final vetting

ready for release
IAO_0000114: pending final vetting

term replaced by
IAO_0000114: pending final vetting

isDefinedBy
OBO foundry unique label: is defined by

Axiom
annotated target: is defined by
comment: This is an experimental annotation
annotated property: OBO foundry unique label
annotated source: isDefinedBy

curation status specification
IAO_0000114: pending final vetting

obsolescence reason specification
IAO_0000114: pending final vetting