OBO Relations Ontology
type: Ontology
version IRI: ro.owl
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
license: https://creativecommons.org/publicdomain/zero/1.0/
version info: 2023-02-22

definition
type: AnnotationProperty

IAO_0000426
type: AnnotationProperty
definition: 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
type: AnnotationProperty
IAO_0000114: pending final vetting

term replaced by
type: AnnotationProperty
IAO_0000114: pending final vetting

defined by construct
type: AnnotationProperty
IAO_0000112: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

temporal interpretation
type: AnnotationProperty
definition: 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_0000112: tooth SubClassOf 'never in taxon' value 'Aves'
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
IAO_0000425: Class: ?X DisjointWith: RO_0002162 some ?Y
defined by construct: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }
sub property of: taxonomic class assertion

mutually spatially disjoint with
type: AnnotationProperty
definition: 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: non-overlapping with
IAO_0000118: shares no parts with
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000425: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
defined by construct: PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . }
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
definition: 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
definition: 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
definition: 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
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
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
sub property of: taxonomic class assertion

present in taxon
type: AnnotationProperty
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
defined by construct: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
sub property of: taxonomic class assertion

defined by inverse
type: AnnotationProperty
sub property of: subset_property

logical macro assertion
type: AnnotationProperty
definition: An assertion that involves at least one OWL object 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
definition: 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
definition: A logical macro assertion whose domain is an IRI for a class
IAO_0000116: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
sub property of: logical macro assertion

logical macro assertion on a property
type: AnnotationProperty
definition: 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
definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
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
definition: 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_0000112: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
definition: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
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))
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
definition: 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_0000112: forelimb always_present_in_taxon Euarchontoglires
definition: 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_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.
IAO_0000118: never lost in
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
definition: 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
definition: 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
definition: 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
definition: 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
definition: 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
definition: 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
definition: 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
definition: 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
definition: Count of number of days intervening between the start of the stage and the time of coitum.
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)
sub property of: has start time value

end, days post coitum
type: AnnotationProperty
definition: 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
definition: 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
definition: 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
definition: 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
definition: 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
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"
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'
creator: https://orcid.org/0000-0002-6601-2165
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
definition: 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: https://orcid.org/0000-0002-6601-2165
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
definition: 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
definition: 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
definition: 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

logical macro assertion involving identity
type: AnnotationProperty
definition: A shortcut relationship that holds between two entities based on their identity criteria
sub property of: logical macro assertion

in approximate one to one relationship with
type: AnnotationProperty
definition: A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
sub property of: logical macro assertion involving identity

is approximately equivalent to
type: AnnotationProperty
definition: x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
IAO_0000232: The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
sub property of: in approximate one to one relationship with

is opposite of
type: AnnotationProperty
IAO_0000112: 'anterior end of organism' is-opposite-of 'posterior end of organism'
IAO_0000112: 'increase in temperature' is-opposite-of 'decrease in temperature'
definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: in approximate one to one relationship with

is indistinguishable from
type: AnnotationProperty
definition: x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: is approximately equivalent to

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

axiom has evidence
type: AnnotationProperty
definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
IAO_0000232: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

axiom contradicted by evidence
type: AnnotationProperty
definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
IAO_0000232: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

is representative IRI for equivalence set
type: AnnotationProperty
IAO_0000112: In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
definition: this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
IAO_0000232: If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
see also: OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
sub property of: logical macro assertion involving identity

nominally disjoint with
type: AnnotationProperty
definition: true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.
creator: https://orcid.org/0000-0002-6601-2165
sub property of: logical macro assertion on an object property

is directional form of
type: AnnotationProperty
definition: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

is homeomorphic for
type: AnnotationProperty
IAO_0000112: part-of is homeomorphic for independent continuants.
definition: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-10-21T19:46:34Z
comment: R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
sub property of: logical macro assertion on an object property

valid_for_go_annotation_extension
type: AnnotationProperty
created by: pg
creation date: 2020-09-22T11:05:29Z
sub property of: subset_property

valid_for_go_gp2term
type: AnnotationProperty
created by: pg
creation date: 2020-09-22T11:05:18Z
sub property of: subset_property

valid_for_go_ontology
type: AnnotationProperty
created by: pg
creation date: 2020-09-22T11:04:12Z
sub property of: subset_property

valid_for_gocam
type: AnnotationProperty
created by: pg
creation date: 2020-09-22T11:05:45Z
sub property of: subset_property

eco subset
type: AnnotationProperty
sub property of: subset_property

subset_property
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

isDefinedBy
OBO foundry unique label: is defined by

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

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
temporal interpretation: axiom holds for all times
is homeomorphic for: continuant
is homeomorphic for: occurrent
is homeomorphic for: independent continuant
is homeomorphic for: realizable entity
is homeomorphic for: quality
is homeomorphic for: specifically dependent continuant
is homeomorphic for: generically dependent continuant
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_gp2term
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
temporal interpretation: axiom holds for all times
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
IAO_0000111: realized in
IAO_0000112: this disease is realized in this disease course
IAO_0000112: this fragility is realized in this shattering
IAO_0000112: this investigator role is realized in this investigation
IAO_0000118: is realized by
IAO_0000118: realized_in
IAO_0000600: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
IAO_0000111: realizes
IAO_0000112: this disease course realizes this disease
IAO_0000112: this investigation realizes this investigator role
IAO_0000112: this shattering realizes this fragility
IAO_0000600: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

obsolete preceded by
type: ObjectProperty
type: TransitiveProperty
comment: accidentally included in BFO 1.2 proposal - should have been BFO_0000062
deprecated: true

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
IAO_0000111: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: eco subset

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: happens during
IAO_0000111: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: eco subset

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
IAO_0000111: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
IAO_0000118: occurs_in
IAO_0000118: unfolds in
IAO_0000118: unfolds_in
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
IAO_0000111: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

derives from part of
type: ObjectProperty
definition: A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
IAO_0000118: inheres_in
temporal interpretation: axiom holds for all times
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
IAO_0000116: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
IAO_0000118: function_of
IAO_0000118: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000112: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
IAO_0000118: is role of
IAO_0000118: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
IAO_0000118: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000112: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
IAO_0000118: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
IAO_0000118: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in_subset: defined by inverse
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

obsolete in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
deprecated: true

obsolete upstream in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: OBSOLETE 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, in which the direction is from the last to the first.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
deprecated: true

obsolete downstream in neural circuit with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
deprecated: true

derives from
type: ObjectProperty
inverse of: derives into
IAO_0000112: this cell derives from this parent cell (cell division)
IAO_0000112: this nucleus derives from this parent nucleus (nuclear division)
IAO_0000114: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
IAO_0000118: derives_from
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

derives into
type: ObjectProperty
IAO_0000112: this parent cell derives into this cell (cell division)
IAO_0000112: this parent nucleus derives into this nucleus (nuclear division)
IAO_0000114: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
IAO_0000118: derives_into
in_subset: eco subset

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
IAO_0000111: is location of
IAO_0000112: my head is the location of my brain
IAO_0000112: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
IAO_0000116: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000118: location_of
temporal interpretation: axiom holds for all times

contained in
type: ObjectProperty
inverse of: contains
domain: material entity
range: independent continuant
property chain axiom: located in
property chain axiom: part of
IAO_0000111: contained in
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_0000118: contained_in
temporal interpretation: axiom holds for all times
in_subset: eco subset

contains
type: ObjectProperty
IAO_0000111: contains
temporal interpretation: axiom holds for all times
in_subset: eco subset

is allergic trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has allergic trigger
domain: material entity
IAO_0000112: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

is autoimmune trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has autoimmune trigger
domain: material entity
definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has allergic trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: material entity
IAO_0000112: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has autoimmune trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: material entity
definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
property chain axiom: part of
IAO_0000111: located in
IAO_0000112: my brain is located in my head
IAO_0000112: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
IAO_0000116: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
IAO_0000116: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000118: located_in
temporal interpretation: axiom holds for all times
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
in_subset: valid_for_go_gp2term

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
IAO_0000116: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
IAO_0000116: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
sub property of: mereotopologically related to
inverse of: has 2D boundary
IAO_0000112: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
IAO_0000116: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
IAO_0000116: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
IAO_0000118: 2D_boundary_of
IAO_0000118: boundary of
IAO_0000118: is 2D boundary of
IAO_0000118: is boundary of
IAO_0000118: surface of
temporal interpretation: axiom holds for all times

aligned with
type: ObjectProperty
type: TransitiveProperty
IAO_0000114: pending final vetting
IAO_0000116: May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
IAO_0000117: https://orcid.org/0000-0002-7073-9172
temporal interpretation: axiom holds for all times

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: immaterial entity
IAO_0000112: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
IAO_0000116: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
IAO_0000116: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has boundary
IAO_0000118: has_2D_boundary
temporal interpretation: axiom holds for all times

electrically_synapsed_to
type: ObjectProperty
sub property of: connected to
definition: A relation that holds between two neurons that are electrically coupled via gap junctions.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

tracheates
type: ObjectProperty
sub property of: contained in
domain: connected anatomical structure
range: connected anatomical structure
definition: 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: https://orcid.org/0000-0002-7073-9172

innervated_by
type: ObjectProperty
inverse of: innervates
domain: connected anatomical structure
range: neuron projection bundle
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

bounding layer of
type: ObjectProperty
sub property of: part of
domain: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has characteristic
    some values from: laminar
range: material entity
definition: 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
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: eco subset
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.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
domain: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
definition: 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.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: eco subset
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.

cell expresses
type: ObjectProperty
sub property of: expresses
domain: cell
definition: 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: https://orcid.org/0000-0002-7073-9172
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

regulates in other organism
type: ObjectProperty
sub property of: causally upstream of or within
domain: process
range: process
definition: 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: https://orcid.org/0000-0002-7073-9172

regulates transport of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: transports or maintains localization of
definition: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: eco subset

occurrent part of
type: ObjectProperty
sub property of: part of
sub property of: causally upstream of or within
domain: occurrent
range: occurrent
definition: A part of relation that applies only between occurrents.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has necessary component activity
type: ObjectProperty
sub property of: has component activity
sub property of: positively regulated by
created by: dos
creation date: 2017-05-24T09:36:08Z
comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, 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.
created by: dos
creation date: 2017-05-24T09:49:21Z

has ligand
type: ObjectProperty
sub property of: has input
definition: A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
created by: dos
creation date: 2017-07-19T17:30:36Z

transports
type: ObjectProperty
sub property of: transports or maintains localization of
definition: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
created by: dos
creation date: 2017-07-20T17:11:08Z

occurs across
type: ObjectProperty
sub property of: has part that occurs in
definition: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
created by: dos
creation date: 2017-07-20T17:19:37Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
database_cross_reference: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
database_cross_reference: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: GOC:dos

in register with
type: ObjectProperty
sub property of: mereotopologically related to
domain: image
range: image
definition: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
created by: dos
creation date: 2017-12-07T12:58:06Z

Axiom
annotated source: in register with
annotated property: definition
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
database_cross_reference: GOC:dos

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: David Osumi-Sutherland
IAO_0000118: <=
in_subset: eco subset
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 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.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: di
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.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 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.

starts before
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: starts during
property chain axiom: obsolete preceded by
IAO_0000117: David Osumi-Sutherland
in_subset: eco subset

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
is direct form of: precedes
in_subset: eco subset
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
IAO_0000117: David Osumi-Sutherland
IAO_0000118: io
in_subset: eco subset
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000118: d
IAO_0000118: during
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam
in_subset: eco subset
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: David Osumi-Sutherland
IAO_0000118: o
IAO_0000118: overlaps
in_subset: eco subset
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

has soma location
type: ObjectProperty
sub property of: overlaps
domain: neuron
range: connected anatomical structure
property chain axiom: part of
IAO_0000114: pending final vetting
definition: Relation between a neuron and an anatomical structure that its soma is part of.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)
temporal interpretation: axiom holds for all times

fasciculates with
type: ObjectProperty
sub property of: overlaps
inverse of: has fasciculating neuron projection
domain: neuron
range: neuron projection bundle
IAO_0000114: pending final vetting
definition: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: fasciculates with
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) ))))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

axon synapses in
type: ObjectProperty
sub property of: has presynaptic terminal in
domain: neuron
property chain axiom: part of
IAO_0000114: pending final vetting
definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed by
type: ObjectProperty
sub property of: receives input from
inverse of: synapsed to
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
IAO_0000114: pending final vetting
definition: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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?)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has plasma membrane part
type: ObjectProperty
sub property of: has part
domain: material anatomical entity
range: material anatomical entity
IAO_0000112: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
IAO_0000114: pending final vetting
definition: 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.
IAO_0000117: https://orcid.org/0000-0001-9990-8331
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-1617-8244
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19243617
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)
temporal interpretation: axiom holds for all times

synapsed_via_type_Ib_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_Ib_bouton
IAO_0000114: pending final vetting
definition: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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))))

synapsed_via_type_Is_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_Is_bouton
IAO_0000114: pending final vetting
definition: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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))))

synapsed_via_type_II_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_II_bouton
IAO_0000114: pending final vetting
definition: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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))))
temporal interpretation: axiom holds for all times
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))))

synapsed_by_via_type_II_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: pending final vetting
definition: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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)))))

synapsed_by_via_type_Ib_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: pending final vetting
definition: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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)))))

has postsynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
inverse of: has presynaptic terminal in
domain: neuron
property chain axiom: part of
IAO_0000114: pending final vetting
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: synapsed in
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))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

releases neurotransmitter
type: ObjectProperty
domain: connected anatomical structure
range: material entity
IAO_0000114: pending final vetting
IAO_0000118: has neurotransmitter

synapsed_by_via_type_Is_bouton
type: ObjectProperty
sub property of: synapsed by
IAO_0000114: pending final vetting
definition: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
IAO_0000117: https://orcid.org/0000-0001-5948-3092
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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)))))

has presynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
domain: neuron
property chain axiom: part of
IAO_0000114: pending final vetting
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000118: synapses in
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?)
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

synapsed_via_type_III_bouton_to
type: ObjectProperty
sub property of: synapsed to
inverse of: synapsed_by_via_type_III_bouton
definition: 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))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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))))

synapsed_by_via_type_III_bouton
type: ObjectProperty
sub property of: synapsed by
definition: Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
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)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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)))))

synapsed to
type: ObjectProperty
sub property of: sends output to
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
IAO_0000114: pending final vetting
definition: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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?)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
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))))

dendrite synapsed in
type: ObjectProperty
sub property of: has postsynaptic terminal in
domain: neuron
property chain axiom: part of
IAO_0000114: pending final vetting
definition: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

has synaptic terminal in
type: ObjectProperty
sub property of: overlaps
domain: neuron
property chain axiom: part of
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-7073-9172
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?)
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_gocam
in_subset: eco subset

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

has fasciculating neuron projection
type: ObjectProperty
sub property of: overlaps
domain: neuron projection bundle
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
IAO_0000114: pending final vetting
definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has fasciculating component
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) ))))))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

innervates
type: ObjectProperty
domain: neuron projection bundle
property chain axiom: part of
IAO_0000114: pending final vetting
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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?)))
temporal interpretation: axiom holds for all times
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
domain: independent continuant
range: independent continuant
IAO_0000114: pending final vetting
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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)
temporal interpretation: axiom holds for all times

partially overlaps
type: ObjectProperty
sub property of: overlaps
IAO_0000114: pending final vetting
definition: 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_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_0000118: proper overlaps
IAO_0000426: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
temporal interpretation: axiom holds for all times
in_subset: eco subset

derived by descent from
type: ObjectProperty
sub property of: evolutionarily related to
inverse of: has derived by descendant
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: 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: ancestral_stucture_of
IAO_0000118: evolutionarily_descended_from

has derived by descendant
type: ObjectProperty
sub property of: evolutionarily related to
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: inverse of derived by descent from
in_subset: defined by inverse

shares ancestor with
type: ObjectProperty
sub property of: evolutionarily related to
type: SymmetricProperty
type: TransitiveProperty
property chain axiom: derived by descent from
property chain axiom: has derived by descendant
IAO_0000114: pending final vetting
definition: 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'
comment: VBO calls this homologous_to

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

only in taxon
type: ObjectProperty
sub property of: in taxon
IAO_0000112: lactation SubClassOf 'only in taxon' some 'Mammalia'
IAO_0000114: pending final vetting
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: organism or virus or viroid
property chain axiom: part of
property chain axiom: has part
property chain axiom: develops from
property chain axiom: expressed in
property chain axiom: has prototype
property chain axiom: capable of
property chain axiom: develops from part of
property chain axiom: has developmental contribution from
property chain axiom: results in developmental progression of
IAO_0000114: pending final vetting
definition: 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: 0000-0001-9227-417X
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
in_subset: eco subset
comment: Connects a biological entity to its taxon of origin.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
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)
temporal interpretation: axiom holds for all times
in_subset: eco subset

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: part of
  some values from: system
range: Restriction
  on property: part of
  some values from: system
property chain axiom:
  inverse of: connects
property chain axiom: connects
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: 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
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: Restriction
  on property: part of
  some values from: system
IAO_0000112: The M8 connects Glasgow and Edinburgh
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: 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_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

attached to part of
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: biomechanically related to
domain: connected anatomical structure
range: connected anatomical structure
property chain axiom: attached to
property chain axiom: part of
definition: 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.
OBO foundry unique label: attached to part of (anatomical structure to anatomical structure)

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

supplies
type: ObjectProperty
sub property of: connected to
definition: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
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_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

drains
type: ObjectProperty
sub property of: connected to
definition: 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.
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_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: pending final vetting
definition: 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.
temporal interpretation: axiom holds for all times
in_subset: eco subset

has phenotype
type: ObjectProperty
sub property of: has phenotype or disease
inverse of: phenotype of
domain: Class
  union of: generically dependent continuant
  union of: material anatomical entity
  union of: disease
range: phenotype
IAO_0000114: pending final vetting
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

phenotype of
type: ObjectProperty
type: FunctionalProperty
IAO_0000114: pending final vetting
definition: inverse of has phenotype
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse
in_subset: eco subset

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
IAO_0000114: pending final vetting
definition: 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
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: inverse of develops from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
in_subset: defined by inverse

gene product of
type: ObjectProperty
sub property of: genomically related to
inverse of: has gene product
domain: independent continuant
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: continuant
range: Class
  union of: generically dependent continuant
  union of: material entity
property chain axiom: ribosomal translation of
property chain axiom: transcribed from
IAO_0000114: pending final vetting
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has gene product
type: ObjectProperty
sub property of: genomically related to
domain: continuant
range: independent continuant
property chain axiom: transcribed to
property chain axiom: ribosomally translates to
IAO_0000112: every HOTAIR lncRNA is the gene product of some HOXC gene
IAO_0000112: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: continuant
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: material anatomical entity
property chain axiom: part of
IAO_0000112: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
domain: Class
  union of: multicellular anatomical structure
  union of: cell
range: Class
  union of: multicellular anatomical structure
  union of: cell
IAO_0000114: pending final vetting
definition: 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 participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000119: FBbt
is direct form of: develops from
has_exact_synonym: has developmental precursor
comment: TODO - add child relations from DOS

parasitoid of
type: ObjectProperty
sub property of: parasite of
inverse of: has parasitoid
definition: A parasite that kills or sterilizes its host

has parasitoid
type: ObjectProperty
sub property of: parasitized by
definition: inverse of parasitoid of
in_subset: defined by inverse

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

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: ends with
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
IAO_0000117: https://orcid.org/0000-0001-7476-6306
IAO_0000117: https://orcid.org/0000-0002-3837-8864
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
IAO_0000600: false
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
OBO foundry unique label: negatively regulates (process to process)
is negative form of: regulates
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
OBO foundry unique label: positively regulates (process to process)
is positive form of: regulates
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

has prototype
type: ObjectProperty
domain: Class
  union of: independent continuant
  union of: process
IAO_0000112: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
IAO_0000112: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
IAO_0000114: pending final vetting
definition: 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_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: TODO: add homeomorphy axiom
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_0000117: https://orcid.org/0000-0002-6601-2165

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
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)".
in_subset: eco subset

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function in

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

obsolete actively participates in
type: ObjectProperty
definition: OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: agent in
term replaced by: process has causal agent
comment: Obsoleted as the inverse property was obsoleted.
deprecated: true

obsolete has active participant
type: ObjectProperty
definition: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has agent
term replaced by: causal agent in process
deprecated: true

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
temporal interpretation: axiom holds for all times

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: https://orcid.org/0000-0002-6601-2165
temporal interpretation: axiom holds for all times
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

Axiom
annotated source: adjacent to
annotated property: IAO_0000112
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

surrounds
type: ObjectProperty
sub property of: adjacent to
IAO_0000114: pending final vetting
definition: inverse of surrounded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165
temporal interpretation: axiom holds for all times
in_subset: defined by inverse

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Allen's interval algebra
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.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: eco subset
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
IAO_0000114: pending final vetting
definition: inverse of starts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: Allen
in_subset: eco subset

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
IAO_0000112: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
IAO_0000114: pending final vetting
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: started by
in_subset: eco subset

develops from part of
type: ObjectProperty
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: part of
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165

develops in
type: ObjectProperty
sub property of: developmentally preceded by
domain: anatomical entity
property chain axiom: directly develops from
property chain axiom: located in
IAO_0000114: pending final vetting
definition: x develops_in y if x is located in y whilst x is developing
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: EHDAA2
IAO_0000119: Jonathan Bard, EHDAA2

obligate parasite of
type: ObjectProperty
sub property of: parasite of
definition: A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.

facultative parasite of
type: ObjectProperty
sub property of: parasite of
definition: A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
IAO_0000114: pending final vetting
definition: inverse of ends with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
in_subset: eco subset

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: finished by
in_subset: eco subset

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: starts with
property chain axiom: occurs in
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts with process that occurs in
in_subset: eco subset

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: ends with
property chain axiom: occurs in
IAO_0000114: pending final vetting
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends with process that occurs in
in_subset: eco subset

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
property chain axiom: starts with
IAO_0000114: pending final vetting
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: consumes
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam
in_subset: eco subset

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
property chain axiom: ends with
IAO_0000114: pending final vetting
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: produces
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam
in_subset: eco subset

stem parasite of
type: ObjectProperty
sub property of: parasite of
definition: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)

root parasite of
type: ObjectProperty
sub property of: parasite of
definition: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)

hemiparasite of
type: ObjectProperty
sub property of: parasite of
definition: A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.

has component participant
type: ObjectProperty
sub property of: has participant
definition: X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.
IAO_0000117: https://orcid.org/0000-0001-9625-1899
IAO_0000232: This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.

has exposure receptor
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
IAO_0000119: ExO:0000001

has exposure stressor
type: ObjectProperty
sub property of: has exposure stimulus
definition: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
IAO_0000119: ExO:0000000

has exposure route
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
IAO_0000119: ExO:0000055

has exposure transport path
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and the course takes from the source to the target.
IAO_0000119: http://purl.obolibrary.org/obo/ExO_0000004

related via exposure to
type: ObjectProperty
sub property of: causally related to
domain: exposure event or process
definition: Any relationship between an exposure event or process and any other entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.

over-expressed in
type: ObjectProperty
sub property of: expressed in
definition: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.

under-expressed in
type: ObjectProperty
sub property of: expressed in
definition: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

has active ingredient
type: ObjectProperty
sub property of: has part
inverse of: active ingredient in
domain: material entity
range: material entity
IAO_0000112: Any portion of roundup 'has active ingredient' some glyphosate
definition: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has_exact_synonym: has active substance
has_related_synonym: has active pharmaceutical ingredient

active ingredient in
type: ObjectProperty
sub property of: part of
definition: inverse of has active ingredient
in_subset: defined by inverse

connecting branch of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
inverse of: has connecting branch
IAO_0000112: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
definition: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
nominally disjoint with: part of

has connecting branch
type: ObjectProperty
sub property of: in branching relationship with
definition: inverse of connecting branch of
nominally disjoint with: has part
in_subset: defined by inverse

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: pending final vetting
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
IAO_0000114: pending final vetting
definition: inverse of has developmental contribution from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse

developmentally induced by
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally induces
domain: material anatomical entity
range: material anatomical entity
IAO_0000114: pending final vetting
definition: 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 material anatomical entity type T to T', where T' develops_from T
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: induced by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
IAO_0000119: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
IAO_0000119: GO:0001759
IAO_0000232: We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]

developmentally induces
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally induce
IAO_0000114: pending final vetting
definition: Inverse of developmentally induced by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
IAO_0000114: pending final vetting
definition: 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_0000116: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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

has biological role
type: ObjectProperty
sub property of: has role
definition: c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)

has application role
type: ObjectProperty
sub property of: has role
definition: c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)

has chemical role
type: ObjectProperty
sub property of: has role
definition: c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in_subset: valid_for_go_gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in_subset: valid_for_go_gp2term

developmentally replaces
type: ObjectProperty
sub property of: developmentally preceded by
IAO_0000114: pending final vetting
definition: 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_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: https://orcid.org/0000-0002-6601-2165
IAO_0000118: replaces

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: pending final vetting
definition: Inverse of developmentally preceded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

part of developmental precursor of
type: ObjectProperty
sub property of: developmentally succeeded by
property chain axiom: part of
property chain axiom: directly develops into
IAO_0000112: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165

ubiquitously expressed in
type: ObjectProperty
sub property of: expressed in
inverse of: ubiquitously expresses
IAO_0000114: pending final vetting
definition: 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_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_0000117: https://orcid.org/0000-0002-6601-2165

expresses
type: ObjectProperty
sub property of: genomically related to
IAO_0000114: pending final vetting
definition: Inverse of 'expressed in'
IAO_0000117: https://orcid.org/0000-0002-6601-2165

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
IAO_0000114: pending final vetting
definition: inverse of ubiquiotously expressed in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: biological_process
range: anatomical entity
IAO_0000114: pending final vetting
definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in development of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in formation of
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in morphogenesis of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
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_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in maturation of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
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_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: pending final vetting
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in disappearance of
type: ObjectProperty
sub property of: results in ending of
IAO_0000112: foramen ovale closure SubClassOf results in disappearance of foramen ovale
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: May be merged into parent relation

results in developmental regression of
type: ObjectProperty
sub property of: results in ending of
IAO_0000112: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: May be merged into parent relation

is treated by substance
type: ObjectProperty
sub property of: causally related to
inverse of: is substance that treats
definition: Inverse of 'is substance that treats'
creator: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse

has habitat
type: ObjectProperty
sub property of: ecologically related to
domain: organism or virus or viroid
range: environmental system
IAO_0000112: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
IAO_0000114: requires discussion
definition: x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
IAO_0000117: https://orcid.org/0000-0002-4366-3088
IAO_0000118: adapted for living in
in_subset: eco subset
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
is positive form of: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
is negative form of: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_gocam

has exposure stimulus
type: ObjectProperty
sub property of: related via exposure to
definition: A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
contributor: https://orcid.org/0000-0001-6996-0040
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-8461-9745
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-06-05T17:35:04Z

evolutionary variant of
type: ObjectProperty
sub property of: evolutionarily related to
IAO_0000117: https://orcid.org/0000-0002-6601-2165

transports or maintains localization of
type: ObjectProperty
sub property of: related via localization to
sub property of: results in changes to anatomical or cellular structure
definition: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: regulates localization of
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
temporal interpretation: axiom holds for all times

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

results in acquisition of features of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
range: connected anatomical structure
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.
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in_subset: eco subset

confers advantage in
type: ObjectProperty
sub property of: ecologically related to
range: environmental system
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: https://orcid.org/0000-0002-6601-2165
IAO_0000118: adapted for
in_subset: eco subset

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
temporal interpretation: axiom holds for all times

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
sub property of: mereotopologically related to
domain: material entity
range: material entity
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)
definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
in_subset: valid_for_go_gp2term

contributes to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of
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_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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
in_subset: valid_for_go_gp2term

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in_subset: valid_for_go_gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: false

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

genomically related to
type: ObjectProperty
domain: continuant
range: continuant
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: actively involved in
IAO_0000118: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: process
range: material entity
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
definition: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
OBO foundry unique label: regulates levels of (process to entity)

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
OBO foundry unique label: regulated by (processual)
in_subset: defined by inverse

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse

related via localization to
type: ObjectProperty
domain: process
range: continuant
definition: A relationship that holds via some process of localization
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is a grouping relation.

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

imports
type: ObjectProperty
sub property of: transports
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_ontology

results in transport along
type: ObjectProperty
sub property of: related via localization to
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in transport across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_ontology

results in growth of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: 'pollen tube growth' results_in growth_of some 'pollen tube'
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to
IAO_0000112: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

exports
type: ObjectProperty
sub property of: transports
definition: 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 end location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_ontology

results in commitment to
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
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.
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in determination of
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
IAO_0000112: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
IAO_0000118: is member of
IAO_0000118: member part of
IAO_0000119: SIO
temporal interpretation: axiom holds for all times

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
IAO_0000119: SIO
temporal interpretation: axiom holds for all times

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse
in_subset: eco subset

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse
in_subset: eco subset

formed as result of
type: ObjectProperty
sub property of: output of
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in structural organization of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
definition: 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: https://orcid.org/0000-0002-6601-2165

results in specification of
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in developmental induction of
type: ObjectProperty
sub property of: results in developmental progression of
definition: 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: https://orcid.org/0000-0002-6601-2165

has dendrite location
type: ObjectProperty
sub property of: overlaps
IAO_0000117: https://orcid.org/0000-0002-6601-2165
source: http://neurolex.org/wiki/Property:DendriteLocation

attached to
type: ObjectProperty
sub property of: connected to
sub property of: attached to part of
type: SymmetricProperty
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
OBO foundry unique label: attached to (anatomical structure to anatomical structure)
in_subset: eco subset

has muscle origin
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: connected anatomical structure
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle origin
annotated property: domain
annotated target: connected anatomical structure
comment: We need to import uberon muscle to create a stricter domain constraint

has muscle insertion
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: connected anatomical structure
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle insertion
annotated property: domain
annotated target: connected anatomical structure
IAO_0000116: We need to import uberon muscle into RO to use as a stricter domain constraint

derived from ancestral fusion of
type: ObjectProperty
sub property of: derived by descent from
IAO_0000112: false
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
has_broad_synonym: has fused element
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.

in branching relationship with
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: material entity
IAO_0000114: requires discussion
definition: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
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)
nominally disjoint with: part of

tributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
IAO_0000112: Deschutes River tributary_of Columbia River
IAO_0000112: inferior epigastric vein tributary_of external iliac vein
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: drains into
IAO_0000118: drains to
IAO_0000118: tributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Tributary
IAO_0000119: http://www.medindia.net/glossary/venous_tributary.htm
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
in_subset: eco subset

distributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
IAO_0000112: Deschutes River distributary_of Little Lava Lake
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: branch of
IAO_0000118: distributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Distributary
in_subset: eco subset
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes

anabranch of
type: ObjectProperty
sub property of: distributary of
sub property of:
  inverse of: tributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
IAO_0000114: requires discussion
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000118: anastomoses with
in_subset: eco subset

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
IAO_0000112: A lump of clay and a statue
definition: x spatially_coextensive_with y if and inly if x and y have the same location
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

branching part of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
inverse of: has branching part
range: Restriction
  on property: has characteristic
  some values from: branched
property chain axiom: distributary of
property chain axiom: main stem of
IAO_0000112: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

main stem of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
IAO_0000112: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'.
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

proper distributary of
type: ObjectProperty
sub property of: distributary of
IAO_0000114: requires discussion
definition: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

proper tributary of
type: ObjectProperty
sub property of: tributary of
IAO_0000114: requires discussion
definition: x proper_tributary_of y iff x tributary_of y and x does not originate from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: requires discussion
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally induce
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: requires discussion
definition: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: requires discussion
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: requires discussion
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has direct input
type: ObjectProperty
sub property of: has input
property chain axiom: starts with
IAO_0000112: 'protein catabolic process' SubClassOf has_direct_input some protein
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly consumes
IAO_0000232: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'

obsolete has indirect input
type: ObjectProperty
IAO_0000114: requires discussion
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

obsolete has direct output
type: ObjectProperty
IAO_0000112: translation SubClassOf has_direct_output some protein
IAO_0000114: requires discussion
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly produces
deprecated: true

obsolete has indirect output
type: ObjectProperty
property chain axiom: causally upstream of
property chain axiom: obsolete has direct output
IAO_0000114: requires discussion
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: requires discussion
definition: inverse of upstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: requires discussion
IAO_0000117: https://orcid.org/0000-0002-6601-2165

obsolete directly activates
type: ObjectProperty
term replaced by: directly positively regulates
comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'.
deprecated: true

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly activates
is indirect form of: positively regulates

obsolete directly inhibits
type: ObjectProperty
term replaced by: directly negatively regulates
comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'.
deprecated: true

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly inhibits
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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 yie…
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is direct form of: causally upstream of

provides input for
type: ObjectProperty
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
definition: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly provides input for
IAO_0000119: causal-relations
OBO foundry unique label: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of or within, positive effect
type: TransitiveProperty
domain: process
range: process
IAO_0000114: requires discussion
definition: transitive form of directly_provides_input_for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
OBO foundry unique label: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: influences (processual)
has_related_synonym: affects

differs in
type: ObjectProperty
IAO_0000116: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: This is an exploratory relation

differs in attribute of
type: ObjectProperty
sub property of: differs in
range: Class
  union of: independent continuant
  union of: process
IAO_0000117: https://orcid.org/0000-0002-6601-2165

differs in attribute
type: ObjectProperty
sub property of: differs in
range: specifically dependent continuant
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
in_subset: defined by inverse

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is positive form of: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
is negative form of: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: 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_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: executes activity in
has_exact_synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dos

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
definition: 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: https://orcid.org/0000-0002-6601-2165

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: 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.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.
has_exact_synonym: in pairwise interaction with
in_subset: eco subset

genetically interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
IAO_0000116: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: binds
IAO_0000118: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: material entity
range: material entity
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: interacts with on organism level
in_subset: eco subset

trophically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
definition: An interaction relationship in which the partners are related via a feeding relationship.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

preys on
type: ObjectProperty
sub property of: trophically interacts with
inverse of: preyed upon by
IAO_0000112: A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
IAO_0000112: Baleen whale preys on krill
definition: An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
IAO_0000117: https://orcid.org/0000-0001-7134-3324
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-3138-4118
IAO_0000118: is subject of predation interaction with
IAO_0000118: preys upon
in_subset: eco subset

symbiotically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
type: SymmetricProperty
property chain axiom: partner in
property chain axiom: is symbiosis
property chain axiom:
  inverse of: partner in
definition: A biotic interaction in which the two organisms live together in more or less intimate association.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
in_subset: eco subset

commensually interacts with
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is commensalism
property chain axiom:
  inverse of: partner in
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
in_subset: eco subset

mutualistically interacts with
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is mutualism
property chain axiom:
  inverse of: partner in
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
in_subset: eco subset

interacts with via parasite-host interaction
type: ObjectProperty
sub property of: symbiotically interacts with
property chain axiom: partner in
property chain axiom: is parasitism
property chain axiom:
  inverse of: partner in
definition: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
in_subset: eco subset

parasite of
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: has host
inverse of: parasitized by
property chain axiom: subject participant in
property chain axiom: is parasitism
property chain axiom:
  inverse of: target participant in
IAO_0000112: Pediculus humanus capitis parasite of human
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: parasitizes
has_exact_synonym: direct parasite of
in_subset: eco subset

parasitized by
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: host of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has parasite
IAO_0000118: parasitised by
has_exact_synonym: directly parasitized by
in_subset: eco subset

participates in a abiotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
IAO_0000112: Porifiera attaches to substrate
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
has_related_synonym: semibiotically interacts with
in_subset: eco subset

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is kinase activity
property chain axiom: has direct input
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
has_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly inhibits
has_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly activates
has_exact_synonym: molecularly increases activity of

transmitted by
type: ObjectProperty
sub property of: ecologically related to
IAO_0000112: all dengue disease transmitted by some mosquito
definition: A relationship that holds between a disease and organism
IAO_0000116: Add domain and range constraints
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has symptom
type: ObjectProperty
sub property of: has phenotype
domain: disease
definition: A relation that holds between a disease or an organism and a phenotype
IAO_0000117: https://orcid.org/0000-0002-6601-2165

host of
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
in_subset: eco subset

has host
type: ObjectProperty
sub property of: symbiotically interacts with
definition: X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

pollinates
type: ObjectProperty
sub property of: mutualistically interacts with
inverse of: pollinated by
IAO_0000112: Bees pollinate Flowers
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: https://orcid.org/0000-0002-6601-2165
IAO_0000118: is subject of pollination interaction with
in_subset: eco subset

pollinated by
type: ObjectProperty
sub property of: mutualistically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has polinator
IAO_0000118: is target of pollination interaction with
in_subset: eco subset

acquires nutrients from
type: ObjectProperty
sub property of: trophically interacts with
inverse of: provides nutrients for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.
in_subset: eco subset

preyed upon by
type: ObjectProperty
sub property of: trophically interacts with
definition: inverse of preys on
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has predator
IAO_0000118: is target of predation interaction with
in_subset: defined by inverse
in_subset: eco subset

is vector for
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: has vector
IAO_0000112: Anopheles is a vector for Plasmodium
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
in_subset: eco subset

has vector
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

partner in
type: ObjectProperty
sub property of: participates in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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

subject participant in
type: ObjectProperty
sub property of: partner in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

target participant in
type: ObjectProperty
sub property of: partner in
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

is symbiosis
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is commensalism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is mutualism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is parasitism
type: ObjectProperty
sub property of: is symbiosis
IAO_0000117: https://orcid.org/0000-0002-6601-2165

provides nutrients for
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

eats
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: is subject of eating interaction with
in_subset: eco subset

is eaten by
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: eaten by
IAO_0000118: is target of eating interaction with
in_subset: eco subset

is evidence for
type: ObjectProperty
sub property of: related via evidence or inference to
inverse of: has evidence
definition: 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: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

composed primarily of
type: ObjectProperty
sub property of: has part
domain: material entity
range: material entity
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
temporal interpretation: axiom holds for all times
in_subset: eco subset

child nucleus of
type: ObjectProperty
sub property of: developmentally preceded by
domain: nucleus
range: nucleus
IAO_0000112: ABal nucleus child nucleus of ABa nucleus (in C elegans)
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

child nucleus of in hermaphrodite
type: ObjectProperty
sub property of: child nucleus of
definition: A child nucleus relationship in which the cells are part of a hermaphroditic organism
IAO_0000117: https://orcid.org/0000-0002-6601-2165

child nucleus of in male
type: ObjectProperty
sub property of: child nucleus of
definition: A child nucleus relationship in which the cells are part of a male organism
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

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

ubiquitinates
type: ObjectProperty
sub property of: molecularly interacts with
property chain axiom: capable of
property chain axiom: is ubiquitination
property chain axiom: has direct input
definition: 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_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

is ubiquitination
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
IAO_0000116: See notes for inverse relation
IAO_0000117: https://orcid.org/0000-0002-6601-2165

sends output to
type: ObjectProperty
sub property of: connected to
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

relation between physical entity and a process or stage
type: ObjectProperty
domain: independent continuant
range: occurrent
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
property chain axiom: existence starts at end of
definition: 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: https://orcid.org/0000-0002-6601-2165

existence starts with
type: ObjectProperty
sub property of: existence starts during
definition: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
definition: 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))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

existence starts and ends during
type: ObjectProperty
sub property of: existence starts during
sub property of: existence ends during
definition: x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. 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)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has_exact_synonym: exists during
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.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
property chain axiom: existence ends at start of
definition: 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: https://orcid.org/0000-0002-6601-2165
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.

existence ends with
type: ObjectProperty
sub property of: existence ends during
definition: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

transformation of
type: ObjectProperty
sub property of: develops from
type: TransitiveProperty
definition: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
IAO_0000117: https://orcid.org/0000-0002-6601-2165

immediate transformation of
type: ObjectProperty
sub property of: directly develops from
sub property of: transformation of
definition: 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: https://orcid.org/0000-0002-6601-2165
is direct form of: transformation of

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: preceded by
property chain axiom: simultaneous with
property chain axiom: existence starts at end of
property chain axiom:
  inverse of: existence starts at end of
definition: 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: https://orcid.org/0000-0002-6601-2165
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.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally succeeded by
property chain axiom: precedes
property chain axiom: simultaneous with
property chain axiom: existence ends at start of
property chain axiom:
  inverse of: existence ends at start of
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: 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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
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.

depends on
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165

towards
type: ObjectProperty
sub property of: depends on
definition: 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
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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
sub property of: has participant
IAO_0000112: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
definition: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has intermediate product
in_subset: eco subset

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
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.

determined by
type: ObjectProperty
sub property of: part of
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
domain: system
range: material entity
IAO_0000112: A coral reef environment is determined by a particular coral reef
definition: 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.
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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/24330602
OBO foundry unique label: determined by (system to material entity)
creator: https://orcid.org/0000-0002-4366-3088
creator: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

determines
type: ObjectProperty
sub property of: causally influences
definition: inverse of determined by
IAO_0000117: https://orcid.org/0000-0002-6601-2165
OBO foundry unique label: determines (material entity to system)
in_subset: defined by inverse
in_subset: eco subset

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between entities
domain: system
range: material entity
property chain axiom: determined by
property chain axiom: part of
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

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

transcribed from
type: ObjectProperty
sub property of: genomically related to
inverse of: transcribed to
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: Class
  union of: generically dependent continuant
  union of: material entity
definition: x is transcribed from y if and only if x is synthesized from template y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

transcribed to
type: ObjectProperty
sub property of: genomically related to
definition: inverse of transcribed from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
in_subset: defined by inverse

ribosomal translation of
type: ObjectProperty
sub property of: genomically related to
inverse of: ribosomally translates to
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: Class
  union of: generically dependent continuant
  union of: material entity
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

ribosomally translates to
type: ObjectProperty
sub property of: genomically related to
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: Class
  union of: generically dependent continuant
  union of: material entity
definition: inverse of ribosomal translation of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267

sequentially related to
type: ObjectProperty
domain: sequentially ordered entity
range: sequentially ordered entity
definition: A relation that holds between two entities that have the property of being sequences or having sequences.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
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_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

sequentially adjacent to
type: ObjectProperty
sub property of: does not overlap sequence of
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
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

has start sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is start sequence of
type: TransitiveProperty
IAO_0000112: Every CDS has as a start sequence the start codon for that transcript
definition: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: started by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is start sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
definition: inverse of has start sequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

has end sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is end sequence of
type: TransitiveProperty
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)
definition: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ended by
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is end sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
definition: inverse of has end sequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

is consecutive sequence of
type: ObjectProperty
sub property of: has subsequence
definition: 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.
IAO_0000116: In the SO paper, this was defined as an instance-type relation
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is sequentially aligned with
type: ObjectProperty
sub property of: sequentially related to
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.
definition: 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: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

bounds sequence of
type: ObjectProperty
sub property of: sequentially related to
inverse of: is bound by sequence of
type: TransitiveProperty
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)
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

is bound by sequence of
type: ObjectProperty
sub property of: sequentially related to
type: TransitiveProperty
definition: inverse of bounds sequence of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract
in_subset: defined by inverse

has subsequence
type: ObjectProperty
sub property of: has part
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of
type: TransitiveProperty
definition: x has subsequence y iff all of the sequence parts of y are sequence parts of x
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: contains
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is subsequence of
type: ObjectProperty
sub property of: part of
sub property of: is bound by sequence of
sub property of: overlaps sequence of
type: TransitiveProperty
definition: inverse of has subsequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: contained by
cites as authority: 006650.abstract
in_subset: defined by inverse

overlaps sequence of
type: ObjectProperty
sub property of: overlaps
sub property of: sequentially related to
type: SymmetricProperty
property chain axiom: has subsequence
property chain axiom: is subsequence of
definition: x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

does not overlap sequence of
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
definition: x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: disconnected from
cites as authority: 006650.abstract

is upstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: inverse of downstream of sequence of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

is downstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

is immediately downstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of
IAO_0000112: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
is direct form of: is downstream of sequence of
cites as authority: 006650.abstract

is immediately upstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of
IAO_0000112: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
definition: inverse of immediately downstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
cites as authority: 006650.abstract

has skeleton
type: ObjectProperty
sub property of: has part
inverse of: skeleton of
type: AsymmetricProperty
type: IrreflexiveProperty
domain: connected anatomical structure
range: material anatomical entity
IAO_0000112: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
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).

Axiom
annotated source: has skeleton
annotated property: range
annotated target: material anatomical entity
IAO_0000116: This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.

results in ending of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
definition: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

hyperparasite of
type: ObjectProperty
sub property of: has host
inverse of: hyperparasitized by
property chain axiom: parasite of
definition: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000116: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
has_narrow_synonym: hyperparasitoid of
has_related_synonym: epiparasite of
in_subset: eco subset

hyperparasitized by
type: ObjectProperty
sub property of: host of
property chain axiom: parasitized by
definition: inverse of hyperparasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has_related_synonym: has epiparasite
has_related_synonym: has hyperparasite
has_related_synonym: hyperparasitoidized by
in_subset: defined by inverse
in_subset: eco subset

allelopath of
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://en.wikipedia.org/wiki/Allelopathy
in_subset: eco subset
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

pathogen of
type: ObjectProperty
sub property of: has host
inverse of: has pathogen
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

has pathogen
type: ObjectProperty
sub property of: host of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

has evidence
type: ObjectProperty
sub property of: related via evidence or inference to
definition: inverse of is evidence for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/25052702
in_subset: defined by inverse
in_subset: eco subset
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.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
OBO foundry unique label: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in movement of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
definition: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000119: causal-relations
OBO foundry unique label: causally influences (entity-centric)

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
domain: connected anatomical structure
range: connected anatomical structure
definition: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.

has muscle antagonist
type: ObjectProperty
sub property of: biomechanically related to
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Wikipedia:Antagonist_(muscle)

has branching part
type: ObjectProperty
sub property of: has part
sub property of: in branching relationship with
type: TransitiveProperty
definition: inverse of branching part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse
in_subset: eco subset

conduit for
type: ObjectProperty
sub property of: overlaps
domain: material entity
range: material entity
definition: 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_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: UBERON:cjm
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.
in_subset: eco subset

lumen of
type: ObjectProperty
sub property of: part of
range: material entity
definition: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:cjm
in_subset: eco subset

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: immaterial entity
definition: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

has modifier
type: ObjectProperty
domain: specifically dependent continuant
range: specifically dependent continuant
definition: A relation that holds between an attribute or a qualifier and another attribute.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
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.
in_subset: eco subset

participates in a biotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
domain: organism or virus or viroid
range: organism or virus or viroid
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

skeleton of
type: ObjectProperty
sub property of: part of
domain: connected anatomical structure
range: connected anatomical structure
definition: inverse of has skeleton
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: defined by inverse

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
OBO foundry unique label: directly regulates (processual)
is direct form of: regulates
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

existence starts at end of
type: ObjectProperty
sub property of: existence starts during or after
definition: holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in closure of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
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.

results in breakdown of
type: ObjectProperty
sub property of: has input
definition: 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

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
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

results in catabolism of
type: ObjectProperty
sub property of: results in breakdown of
definition: 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.

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
sub property of: results in changes to anatomical or cellular structure
definition: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c

existence ends at start of
type: ObjectProperty
sub property of: existence ends during or before
definition: holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations

capable of inhibiting or preventing pathological process
type: ObjectProperty
sub property of: capable of negatively regulating
IAO_0000112: pazopanib -> pathological angiogenesis
definition: 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_0000118: treats
IAO_0000119: causal-relations
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.

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

capable of upregulating or causing pathological process
type: ObjectProperty
sub property of: capable of positively regulating
IAO_0000112: benzene -> cancer [CHEBI]
definition: 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.
IAO_0000118: causes disease
IAO_0000119: causal-relations

is substance that treats
type: ObjectProperty
sub property of: capable of inhibiting or preventing pathological process
definition: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
IAO_0000118: treats
IAO_0000119: causal-relations

is marker for
type: ObjectProperty
sub property of: correlated with
definition: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
IAO_0000116: May be ceded to OBI

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

obsolete related via dependence to
type: ObjectProperty
definition: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or 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.
deprecated: true

correlated with
type: ObjectProperty
definition: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
IAO_0000232: Groups both positive and negative correlation

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
IAO_0000112: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
definition: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
comment: In the Gene Ontology association model, this corresponds to the With/From field

has model
type: ObjectProperty
inverse of: has role in modeling
definition: Inverse of is-model-of

related via evidence or inference to
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is a grouping relation.

visits
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: visited by

visited by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

visits flowers of
type: ObjectProperty
sub property of: visits
inverse of: has flowers visited by

has flowers visited by
type: ObjectProperty
sub property of: visited by

lays eggs in
type: ObjectProperty
sub property of: parasite of
sub property of: visits
inverse of: has eggs laid in by

has eggs laid in by
type: ObjectProperty
sub property of: parasitized by
sub property of: visited by

kills
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
inverse of: is killed by
IAO_0000119: https://github.com/jhpoelen/eol-globi-data/issues/143

is killed by
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
IAO_0000119: causal-relations
OBO foundry unique label: directly positively regulates (process to process)
is positive form of: directly regulates
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
IAO_0000119: causal-relations
OBO foundry unique label: directly negatively regulates (process to process)
is negative form of: directly regulates
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

ectoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has ectoparasite
definition: A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
IAO_0000119: Types

has ectoparasite
type: ObjectProperty
sub property of: parasitized by
definition: inverse of ectoparasite of
in_subset: defined by inverse

endoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has endoparasite
IAO_0000119: Types
IAO_0000119: A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
has_related_synonym: lives inside of

has endoparasite
type: ObjectProperty
sub property of: parasitized by

mesoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: has mesoparasite
definition: A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite

has mesoparasite
type: ObjectProperty
sub property of: parasitized by
definition: inverse of mesoparasite of
in_subset: defined by inverse

intercellular endoparasite of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intercellular endoparasite
definition: A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
IAO_0000119: Types

has intercellular endoparasite
type: ObjectProperty
sub property of: has endoparasite
definition: inverse of intercellular endoparasite of
in_subset: defined by inverse

intracellular endoparasite of
type: ObjectProperty
sub property of: endoparasite of
inverse of: has intracellular endoparasite
definition: A sub-relation of endoparasite-of in which the parasite inhabits host cells.
IAO_0000119: Types

has intracellular endoparasite
type: ObjectProperty
sub property of: has endoparasite
definition: inverse of intracellular endoparasite of
in_subset: defined by inverse

co-roosts with
type: ObjectProperty
sub property of: ecologically co-occurs with
type: SymmetricProperty
definition: Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
IAO_0000119: Communal roosting

produces
type: ObjectProperty
inverse of: produced by
domain: material entity
range: material entity
property chain axiom:
  inverse of: occurs in
property chain axiom: has output
IAO_0000114: pending final vetting
definition: 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: https://orcid.org/0000-0001-9114-8737
in_subset: eco subset
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.

produced by
type: ObjectProperty
domain: material entity
range: material entity
IAO_0000114: pending final vetting
definition: a produced_by b iff some process that occurs_in b has_output a.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in_subset: eco subset

represses expression of
type: ObjectProperty
sub property of: directly negatively regulates activity of
domain: material entity
range: material entity
definition: Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

increases expression of
type: ObjectProperty
sub property of: directly positively regulates activity of
domain: material entity
range: material entity
definition: Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

has role in modeling
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
IAO_0000117: https://orcid.org/0000-0002-1048-5019
IAO_0000118: is used to study
comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate.

causes or contributes to condition
type: ObjectProperty
sub property of: causally related to
IAO_0000112: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
IAO_0000116: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

causes condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.

contributes to condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.

contributes to severity of condition
type: ObjectProperty
sub property of: contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
IAO_0000118: contributes to expressivity of condition

contributes to frequency of condition
type: ObjectProperty
sub property of: contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
IAO_0000118: contributes to penetrance of condition

ameliorates condition
type: ObjectProperty
sub property of: contributes to severity of condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
IAO_0000118: is preventative for condition
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

correlated with condition
type: ObjectProperty
sub property of: correlated with
definition: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

exacerbates condition
type: ObjectProperty
sub property of: contributes to severity of condition
definition: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.

condition ameliorated by
type: ObjectProperty
sub property of: causally related to
definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.

condition exacerbated by
type: ObjectProperty
sub property of: causally related to
definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.

condition has genetic basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is genetic basis for condition
domain: realizable entity
range: Class
  union of: process
  union of: quality
  union of: material entity
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:38:20Z

has material basis in gain of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal gain of function germline mutation of in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:45:20Z

has material basis in loss of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal loss of function germline mutation of in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:45:37Z

has material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:45:54Z

has material basis in somatic mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal somatic mutation in
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:46:07Z

has major susceptibility factor
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal susceptibility factor for
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:46:26Z

has partial material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation partially giving rise to
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:46:57Z

has primary input or output
type: ObjectProperty
sub property of: has participant
definition: p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-12-13T11:26:17Z
in_subset: valid_for_go_ontology

has primary output
type: ObjectProperty
sub property of: has output
sub property of: has primary input or output
definition: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-12-13T11:26:32Z
in_subset: valid_for_go_ontology

Axiom
annotated source: has primary output
annotated property: definition
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

has primary input
type: ObjectProperty
sub property of: has input
sub property of: has primary input or output
definition: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-12-13T11:26:56Z
in_subset: valid_for_go_ontology

Axiom
annotated source: has primary input
annotated property: definition
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

is genetic basis for condition
type: ObjectProperty
sub property of: is basis for realizable
range: realizable entity
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:53:08Z

is causal gain of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:55:51Z

is causal loss of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:56:06Z

is causal germline mutation in
type: ObjectProperty
sub property of: causes condition
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:56:40Z

is causal somatic mutation in
type: ObjectProperty
sub property of: causes condition
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:57:07Z

is causal susceptibility factor for
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:57:43Z

is causal germline mutation partially giving rise to
type: ObjectProperty
sub property of: contributes to condition
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T02:58:43Z

realizable has basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is basis for realizable
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:20:01Z

is basis for realizable
type: ObjectProperty
sub property of: causally related to
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:20:29Z

disease has basis in
type: ObjectProperty
sub property of: realizable has basis in
sub property of: causal relationship with disease as subject
domain: disease
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:26:47Z

disease has basis in dysfunction of
type: ObjectProperty
sub property of: disease has basis in
range: material anatomical entity
definition: A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
OBO foundry unique label: disease has basis in dysfunction of (disease to anatomical structure)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:29:32Z

disease has basis in disruption of
type: ObjectProperty
sub property of: disease has basis in
range: process
definition: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
OBO foundry unique label: disease has basis in disruption of (disease to process)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:37:52Z

disease has basis in feature
type: ObjectProperty
sub property of: has phenotype
sub property of: disease has basis in
domain: disease
range: Class
  union of: disease
  union of: phenotype
definition: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:46:07Z

causal relationship with disease as subject
type: ObjectProperty
sub property of: causally related to
sub property of: disease relationship
domain: disease
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:50:54Z

disease causes disruption of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: disease
range: process
property chain axiom: part of
property chain axiom: disease causes dysfunction of
property chain axiom: capable of
definition: A relationship between a disease and a process where the disease process disrupts the execution of the process.
OBO foundry unique label: disease causes disruption of (disease to process)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:51:09Z

disease causes dysfunction of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: disease
range: material anatomical entity
property chain axiom: part of
OBO foundry unique label: disease causes dysfunction of (disease to anatomical entity)
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:58:20Z

disease has location
type: ObjectProperty
sub property of: disease relationship
domain: disease
range: independent continuant
range: Class
  union of: material anatomical entity
  union of: immaterial anatomical entity
definition: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
IAO_0000116: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
IAO_0000232: This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T04:06:02Z

disease has inflammation site
type: ObjectProperty
sub property of: disease has location
domain: disease
range: independent continuant
range: Class
  union of: material anatomical entity
  union of: immaterial anatomical entity
definition: A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:37:31Z

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: material entity
property chain axiom: realized in response to
property chain axiom: has input
definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:45:49Z

disease has feature
type: ObjectProperty
sub property of: disease relationship
domain: disease
range: Class
  union of: disease
  union of: phenotype
definition: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:50:53Z

disease arises from alteration in structure
type: ObjectProperty
sub property of: disease has basis in
range: connected anatomical structure
definition: A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:58:44Z

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
is positive form of: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:30Z
in_subset: valid_for_go_gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
is negative form of: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:51Z
in_subset: valid_for_go_gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
is positive form of: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:14Z
in_subset: valid_for_go_gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
is negative form of: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:22Z
in_subset: valid_for_go_gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
is negative form of: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
is positive form of: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

DEPRECATED inheres in
type: ObjectProperty
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
deprecated: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

has driver
type: ObjectProperty
definition: A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.
contributor: https://orcid.org/0000-0001-8910-9851

has disease driver
type: ObjectProperty
sub property of: has driver
definition: A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.
contributor: https://orcid.org/0000-0001-8910-9851

epiphyte of
type: ObjectProperty
sub property of: symbiotically interacts with
inverse of: has epiphyte
definition: An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
IAO_0000119: https://en.wikipedia.org/wiki/Epiphyte

has epiphyte
type: ObjectProperty
sub property of: symbiotically interacts with
definition: inverse of epiphyte of
in_subset: defined by inverse

kleptoparasite of
type: ObjectProperty
sub property of: parasite of
inverse of: kleptoparasitized by
definition: A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
IAO_0000119: https://en.wikipedia.org/wiki/Kleptoparasitism

kleptoparasitized by
type: ObjectProperty
sub property of: parasitized by
definition: inverse of kleptoparasite of
in_subset: defined by inverse

creates habitat for
type: ObjectProperty
sub property of: ecologically related to
domain: organism or virus or viroid
range: organism or virus or viroid
definition: An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.

ecologically co-occurs with
type: ObjectProperty
sub property of: ecologically related to
type: SymmetricProperty
domain: organism or virus or viroid
range: organism or virus or viroid
definition: An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.

lays eggs on
type: ObjectProperty
sub property of: visits
inverse of: has eggs laid on by
definition: An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.

has eggs laid on by
type: ObjectProperty
sub property of: visited by
definition: inverse of lays eggs on

has substance added
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
IAO_0000112: muffin 'has substance added' some 'baking soda'
IAO_0000114: requires discussion
definition: "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
IAO_0000116: The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

has substance removed
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
IAO_0000112: 'egg white' 'has substance removed' some 'egg yolk'
IAO_0000114: requires discussion
definition: "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

immersed in
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
IAO_0000112: sardines 'immersed in' some 'oil and mustard'
IAO_0000114: requires discussion
definition: "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

has consumer
type: ObjectProperty
domain: material entity
range: organism or virus or viroid
IAO_0000112: sardine has consumer some homo sapiens
IAO_0000114: requires discussion
definition: 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

has primary substance added
type: ObjectProperty
sub property of: has substance added
type: IrreflexiveProperty
IAO_0000112: bread 'has primary substance added' some 'flour'
IAO_0000114: requires discussion
definition: 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
IAO_0000117: https://orcid.org/0000-0002-8844-9165

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: process
property chain axiom: realized in
property chain axiom: causally downstream of
IAO_0000112: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
IAO_0000112: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
IAO_0000112: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: https://orcid.org/0000-0001-6996-0040
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-7073-9172
contributor: https://orcid.org/0000-0002-8461-9745
has_exact_synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: has_exact_synonym
annotated target: triggered by process
database_cross_reference: RO:cjm

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
property chain axiom: characteristic of
property chain axiom: is concretized as
IAO_0000112: Genetic information generically depend on molecules of DNA.
IAO_0000112: The novel *War and Peace* generically depends on this copy of the novel.
IAO_0000112: The pattern shared by chess boards generically depends on any chess board.
IAO_0000112: The score of a symphony g-depends on a copy of the score.
IAO_0000112: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
IAO_0000119: [072-ISO]
has_exact_synonym: g-depends on

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
property chain axiom: concretizes
property chain axiom: has characteristic
IAO_0000112: Molecules of DNA are carriers of genetic information.
IAO_0000112: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
IAO_0000112: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
IAO_0000119: [072-ISO]

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

regulates quantity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly regulates activity of
type: ObjectProperty
sub property of: regulates activity of
domain: material entity
range: material entity
definition: The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

decreases by repression quantity of
type: ObjectProperty
sub property of: indirectly negatively regulates quantity of
domain: material entity
range: material entity
definition: The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

increases by expression quantity of
type: ObjectProperty
sub property of: indirectly positively regulates quantity of
domain: material entity
range: material entity
definition: The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

directly positively regulates quantity of
type: ObjectProperty
sub property of: directly regulates quantity of
domain: material entity
range: material entity
definition: The entity A has an activity that directly positively regulates the quantity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

directly negatively regulates quantity of
type: ObjectProperty
sub property of: directly regulates quantity of
domain: material entity
range: material entity
definition: The entity A has an activity that directly negatively regulates the quantity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly positively regulates activity of
type: ObjectProperty
sub property of: indirectly regulates activity of
domain: material entity
range: material entity
definition: The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: indirectly activates

destabilizes quantity of
type: ObjectProperty
sub property of: directly negatively regulates quantity of
domain: material entity
range: material entity
IAO_0000112: AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
definition: An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

stabilizes quantity of
type: ObjectProperty
sub property of: directly positively regulates quantity of
domain: material entity
range: material entity
IAO_0000112: AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
definition: An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly negatively regulates activity of
type: ObjectProperty
sub property of: indirectly regulates activity of
definition: The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: indirectly inhibits

directly regulates quantity of
type: ObjectProperty
sub property of: regulates quantity of
definition: The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly regulates quantity of
type: ObjectProperty
sub property of: regulates quantity of
definition: The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly negatively regulates quantity of
type: ObjectProperty
sub property of: indirectly regulates quantity of
definition: The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly positively regulates quantity of
type: ObjectProperty
sub property of: indirectly regulates quantity of
definition: The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

has small molecule regulator
type: ObjectProperty
sub property of: has participant
inverse of: is small molecule regulator of
definition: a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
created by: pg
creation date: 2020-04-22T20:27:26Z

has small molecule activator
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule activator of
definition: a relation between a process and a continuant, in which the process is activated by the small molecule continuant
created by: pg
creation date: 2020-04-22T20:28:37Z

has small molecule inhibitor
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule inhibitor of
definition: a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
created by: pg
creation date: 2020-04-22T20:28:54Z

acts on population of
type: ObjectProperty
sub property of: has participant
definition: p acts on population of c iff c' is a collection, has members of type c, and p has participant c
created by: pg
creation date: 2020-06-08T17:21:33Z
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

is small molecule regulator of
type: ObjectProperty
sub property of: capable of regulating
definition: a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
created by: pg
creation date: 2020-06-24T13:15:17Z

is small molecule activator of
type: ObjectProperty
sub property of: capable of positively regulating
sub property of: is small molecule regulator of
definition: a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
created by: pg
creation date: 2020-06-24T13:15:26Z

is small molecule inhibitor of
type: ObjectProperty
sub property of: capable of negatively regulating
sub property of: is small molecule regulator of
definition: a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
created by: pg
creation date: 2020-06-24T13:15:35Z

results in adhesion of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
definition: The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.
created by: pg
creation date: 2020-08-27T08:13:59Z

results in fusion of
type: ObjectProperty
sub property of: results in organization of
created by: pg
creation date: 2021-02-26T07:28:29Z
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_go_ontology
in_subset: valid_for_gocam

constitutively upstream of
type: ObjectProperty
sub property of: causally upstream of, positive effect
definition: p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.
created by: pg
creation date: 2022-09-26T06:01:01Z
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_gocam

removes input for
type: ObjectProperty
sub property of: causally upstream of, negative effect
definition: p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.
created by: pg
creation date: 2022-09-26T06:06:20Z
in_subset: valid_for_go_annotation_extension
in_subset: valid_for_gocam

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
definition: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
created by: pg
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: pg
creation date: 2022-09-26T06:08:01Z

has synaptic IO in region
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:26:52Z
has_exact_synonym: has synaptic input or output in

receives synaptic input in region
type: ObjectProperty
sub property of: has postsynaptic terminal in
sub property of: has synaptic IO in region
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:42:23Z

sends synaptic output to region
type: ObjectProperty
sub property of: has presynaptic terminal in
sub property of: has synaptic IO in region
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:45:06Z

has synaptic IO throughout
type: ObjectProperty
sub property of: has synaptic IO in region
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:52:19Z

receives synaptic input throughout
type: ObjectProperty
sub property of: receives synaptic input in region
sub property of: has synaptic IO throughout
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:55:36Z

sends synaptic output throughout
type: ObjectProperty
sub property of: sends synaptic output to region
sub property of: has synaptic IO throughout
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-17T09:57:27Z

has sensory dendrite in
type: ObjectProperty
sub property of: has dendrite location
domain: sensory neuron
property chain axiom: part of
definition: Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2020-07-20T12:10:09Z
has_exact_synonym: has sensory dendrite location
has_exact_synonym: has sensory terminal in
has_exact_synonym: has sensory terminal location

receives synaptic input from neuron
type: ObjectProperty
sub property of: synapsed by
inverse of: sends synaptic output to cell
definition: A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2021-05-26T08:40:18Z

sends synaptic output to cell
type: ObjectProperty
sub property of: synapsed to
definition: A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.
created by: http://orcid.org/0000-0002-1373-1705
creation date: 2021-05-26T08:41:07Z
comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.

disease has infectious agent
type: ObjectProperty
sub property of: disease has basis in
definition: A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.
created by: http://orcid.org/0000-0001-5208-3432

has exemplar data
type: ObjectProperty
sub property of: topObjectProperty
inverse of: exemplar data of
property chain axiom: subcluster of
IAO_0000112: transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])
definition: A relation between a material entity and some data in which the data is taken as exemplifying the material entity.
IAO_0000116: C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C.
IAO_0000117: https://orcid.org/0000-0002-5260-9315
IAO_0000232: This relation is not meant to capture the relation between occurrents and data.

exemplar data of
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000117: https://orcid.org/0000-0002-5260-9315

subcluster of
type: ObjectProperty
sub property of: part of
type: TransitiveProperty
definition: A relation between a group and another group it is part of but does not fully constitute.
IAO_0000116: X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
IAO_0000117: https://orcid.org/0000-0001-7258-9596
IAO_0000232: This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics.

has characterizing marker set
type: ObjectProperty
domain: cell
IAO_0000112: 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1').
IAO_0000112: transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3.
definition: A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
IAO_0000116: C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
IAO_0000232: This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context.
contributor: https://orcid.org/0000-0001-7258-9596
has_exact_synonym: has marker gene combination
has_exact_synonym: has marker signature set

different in magnitude relative to
type: ObjectProperty
domain: quality
range: quality
definition: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: different in magnitude relative to
annotated property: definition
annotated target: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

increased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: quality
range: quality
definition: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.

Axiom
annotated source: increased in magnitude relative to
annotated property: definition
annotated target: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

decreased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: quality
range: quality
definition: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.

Axiom
annotated source: decreased in magnitude relative to
annotated property: definition
annotated target: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

similar in magnitude relative to
type: ObjectProperty
definition: q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: similar in magnitude relative to
annotated property: definition
annotated target: q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

has relative magnitude
type: ObjectProperty

has cross section
type: ObjectProperty
definition: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

Axiom
annotated source: has cross section
annotated property: definition
annotated target: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

reciprocal of
type: ObjectProperty
definition: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

Axiom
annotated source: reciprocal of
annotated property: definition
annotated target: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

has high plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: cell
IAO_0000112: 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
definition: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
contributor: http://orcid.org/0000-0003-1617-8244
contributor: http://orcid.org/0000-0003-1940-6740

Axiom
annotated source: has high plasma membrane amount
annotated property: definition
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
database_cross_reference: PMID:19243617

has low plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: cell
IAO_0000112: 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
definition: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
contributor: http://orcid.org/0000-0003-1617-8244
contributor: http://orcid.org/0000-0003-1940-6740

Axiom
annotated source: has low plasma membrane amount
annotated property: definition
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
database_cross_reference: PMID:19243617

has phenotype or disease
type: ObjectProperty
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.
contributor: http://orcid.org/0000-0002-7463-6306
date: 2021-11-05T17:30:14Z

has disease
type: ObjectProperty
sub property of: has phenotype or disease
definition: A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
contributor: http://orcid.org/0000-0002-7463-6306
date: 2021-11-05T17:30:44Z

has exposure medium
type: ObjectProperty
sub property of: related via exposure to
definition: X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.
IAO_0000119: ExO:0000083
date: 2021-12-14T20:41:45Z
created by: https://orcid.org/0000-0002-7463-6306

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000112: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
IAO_0000117: https://orcid.org/0000-0001-9625-1899
IAO_0000117: https://orcid.org/0000-0003-2620-0345
IAO_0000232: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
IAO_0000232: See github ticket https://github.com/oborel/obo-relations/issues/497
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

is myristoyltransferase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
definition: Helper relation for OWL definition of RO:0018002 myristoylates
contributor: https://orcid.org/0000-0003-4423-4370

myristoylates
type: ObjectProperty
sub property of: molecularly interacts with
inverse of: myristoylated by
property chain axiom: capable of
property chain axiom: is myristoyltransferase activity
property chain axiom: has direct input
definition: A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input
conforms to: ObjectPropertyDefinedByInteractionProcess
contributor: https://orcid.org/0000-0003-4423-4370

myristoylated by
type: ObjectProperty
definition: inverse of myristoylates
contributor: https://orcid.org/0000-0003-4423-4370

is agonist of
type: ObjectProperty
sub property of: directly positively regulates activity of
IAO_0000112: mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)
definition: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor
creator: https://orcid.org/0000-0003-4423-4370

is inverse agonist of
type: ObjectProperty
sub property of: directly negatively regulates activity of
IAO_0000112: pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)
definition: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level
creator: https://orcid.org/0000-0003-4423-4370

is antagonist of
type: ObjectProperty
sub property of: directly negatively regulates activity of
IAO_0000112: tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)
definition: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level
creator: https://orcid.org/0000-0003-4423-4370

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

confers susceptibility to condition
type: ObjectProperty
sub property of: contributes to condition
definition: Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.
created by: http://orcid.org/0000-0002-4142-7153

disease relationship
type: ObjectProperty
definition: This relation groups relations between diseases and any other kind of entity.
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-09-26T00:00:32Z

results in changes to anatomical or cellular structure
type: ObjectProperty
sub property of: has participant
definition: p has anatomical participant c iff p has participant c, and c is an anatomical entity
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-09-26T01:08:58Z

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
IAO_0000116: TODO: Add homeomorphy axiom
is homeomorphic for: continuant
is homeomorphic for: occurrent
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000041
database_cross_reference: SO:similar_to
has_exact_synonym: sameness
has_exact_synonym: similar to
has_related_synonym: correspondence
has_related_synonym: resemblance

Axiom
annotated source: in similarity relationship with
annotated property: definition
annotated target: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
database_cross_reference: HOM_0000000
database_cross_reference: BGEE:curator

Axiom
annotated source: in similarity relationship with
annotated property: has_related_synonym
annotated target: correspondence
database_cross_reference: http://dx.doi.org/10.1007/BF02814479

in homology relationship with
type: ObjectProperty
sub property of: shares ancestor with
sub property of: in similarity relationship with
type: SymmetricProperty
property disjoint with: in homoplasy relationship with
definition: Similarity that results from common evolutionary origin.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homologous to
comment: This broad definition encompasses all the working definitions proposed so far in the literature.

Axiom
annotated source: in homology relationship with
annotated property: definition
annotated target: Similarity that results from common evolutionary origin.
database_cross_reference: bies.950180611
database_cross_reference: jmor.1051730307
database_cross_reference: http://dx.doi.org/10.1007/BF02814480
database_cross_reference: HOM_0000001

in homoplasy relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
definition: Similarity that results from independent evolution.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homoplasous to
has_related_synonym: analogy

Axiom
annotated source: in homoplasy relationship with
annotated property: definition
annotated target: Similarity that results from independent evolution.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000002

in homocracy relationship with
type: ObjectProperty
sub property of: evolutionarily related to
sub property of: in similarity relationship with
type: SymmetricProperty
definition: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000075
has_exact_synonym: homocracous to
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.

Axiom
annotated source: in homocracy relationship with
annotated property: definition
annotated target: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: s00427-003-0301-4
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000003

in convergence relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
definition: Homoplasy that involves different underlying mechanisms or structures.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: analogy
comment: Convergence usually implies a notion of adaptation.

Axiom
annotated source: in convergence relationship with
annotated property: definition
annotated target: Homoplasy that involves different underlying mechanisms or structures.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000004

in parallelism relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
definition: Homoplasy that involves homologous underlying mechanisms or structures.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: parallel evolution
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.

Axiom
annotated source: in parallelism relationship with
annotated property: definition
annotated target: Homoplasy that involves homologous underlying mechanisms or structures.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000005

in structural homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
definition: Homology that is defined by similarity with regard to selected structural parameters.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000071
database_cross_reference: MI:2163
has_exact_synonym: structural homologous to
has_related_synonym: idealistic homology

Axiom
annotated source: in structural homology relationship with
annotated property: definition
annotated target: Homology that is defined by similarity with regard to selected structural parameters.
database_cross_reference: j.jhevol.2006.11.014
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000006
database_cross_reference: ISBN:0123195837

in historical homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
definition: Homology that is defined by common descent.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_broad_synonym: homology
database_cross_reference: ECO:0000080
database_cross_reference: RO_proposed_relation:homologous_to
database_cross_reference: SO:0000330
database_cross_reference: SO:0000853
database_cross_reference: SO:0000857
database_cross_reference: SO:homologous_to
database_cross_reference: TAO:homologous_to
has_exact_synonym: cladistic homology
has_exact_synonym: historical homologous to
has_exact_synonym: phylogenetic homology
has_exact_synonym: taxic homology
has_related_synonym: true homology

Axiom
annotated source: in historical homology relationship with
annotated property: definition
annotated target: Homology that is defined by common descent.
database_cross_reference: S0169-5347(97)01125-7
database_cross_reference: HOM_0000007
database_cross_reference: ISBN:0123195837

in biological homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
definition: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000067
has_exact_synonym: biological homologous to
has_related_synonym: transformational homology
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.

Axiom
annotated source: in biological homology relationship with
annotated property: definition
annotated target: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
database_cross_reference: S0169-5347(97)01125-7
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000008

in reversal relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
definition: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: atavism
has_exact_synonym: rudiment
has_related_synonym: reversion

Axiom
annotated source: in reversal relationship with
annotated property: definition
annotated target: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000009

in syntenic homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
definition: Structural homology that is detected by similarity in content and organization between chromosomes.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: MeSH:Synteny
database_cross_reference: SO:0000860
database_cross_reference: SO:0005858
has_exact_synonym: syntenic homologous to
has_related_synonym: synteny

Axiom
annotated source: in syntenic homology relationship with
annotated property: definition
annotated target: Structural homology that is detected by similarity in content and organization between chromosomes.
database_cross_reference: HOM_0000010
database_cross_reference: MeSH:Synteny

in paralogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
property disjoint with: in orthology relationship with
definition: Historical homology that involves genes that diverged after a duplication event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: SO:0000854
database_cross_reference: SO:0000859
database_cross_reference: SO:paralogous_to
has_exact_synonym: paralogous to

Axiom
annotated source: in paralogy relationship with
annotated property: definition
annotated target: Historical homology that involves genes that diverged after a duplication event.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000011
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in syntenic paralogy relationship with
type: ObjectProperty
sub property of: in syntenic homology relationship with
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that involves sets of syntenic blocks.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: syntenic paralogous to
has_related_synonym: duplicon
has_related_synonym: paralogon

Axiom
annotated source: in syntenic paralogy relationship with
annotated property: definition
annotated target: Paralogy that involves sets of syntenic blocks.
database_cross_reference: 1471-213X-7-100
database_cross_reference: HOM_0000012
database_cross_reference: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y

in syntenic orthology relationship with
type: ObjectProperty
sub property of: in syntenic homology relationship with
type: SymmetricProperty
definition: Syntenic homology that involves chromosomes of different species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: syntenic orthologous to

Axiom
annotated source: in syntenic orthology relationship with
annotated property: definition
annotated target: Syntenic homology that involves chromosomes of different species.
database_cross_reference: gr.6380007
database_cross_reference: HOM_0000013

in partial homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
definition: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: fractional homology
has_exact_synonym: partial homologous to
has_exact_synonym: segmental homology
has_related_synonym: mixed homology
has_related_synonym: modular homology
has_related_synonym: partial correspondence
has_related_synonym: percent homology

Axiom
annotated source: in partial homology relationship with
annotated property: definition
annotated target: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
database_cross_reference: HOM_0000014
database_cross_reference: ISBN:0123195837
database_cross_reference: ISBN:978-0471984931

in protein structural homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
definition: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: MeSH:Structural_Homology,_Protein
has_exact_synonym: protein structural homologous to

Axiom
annotated source: in protein structural homology relationship with
annotated property: definition
annotated target: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
database_cross_reference: 0022-2836(76)90195-9
database_cross_reference: HOM_0000015

in non functional homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
property disjoint with: in equivalogy relationship with
definition: Structural homology that involves a pseudogenic feature and its functional ancestor.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_broad_synonym: pseudogene
database_cross_reference: SO:non_functional_homolog_of
has_exact_synonym: non functional homologous to

Axiom
annotated source: in non functional homology relationship with
annotated property: definition
annotated target: Structural homology that involves a pseudogenic feature and its functional ancestor.
database_cross_reference: HOM_0000016
database_cross_reference: SO:non_functional_homolog_of

in orthology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves genes that diverged after a speciation event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:00000060
database_cross_reference: SO:0000855
database_cross_reference: SO:0000858
database_cross_reference: SO:orthologous_to
has_exact_synonym: orthologous to
comment: The term is sometimes also used for anatomical structures.

Axiom
annotated source: in orthology relationship with
annotated property: definition
annotated target: Historical homology that involves genes that diverged after a speciation event.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000017
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in xenology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: xenologous to
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).

Axiom
annotated source: in xenology relationship with
annotated property: definition
annotated target: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000018

in 1 to 1 homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves two members sharing no other homologs in the lineages considered.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to 1 homologous to
has_exact_synonym: 1:1 homology
has_exact_synonym: one-to-one homology

Axiom
annotated source: in 1 to 1 homology relationship with
annotated property: definition
annotated target: Historical homology that involves two members sharing no other homologs in the lineages considered.
database_cross_reference: HOM_0000019
database_cross_reference: BGEE:curator

in 1 to 1 orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in 1 to 1 homology relationship with
type: SymmetricProperty
definition: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to 1 orthologous to
has_exact_synonym: 1:1 orthology
has_exact_synonym: one-to-one orthology

Axiom
annotated source: in 1 to 1 orthology relationship with
annotated property: definition
annotated target: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: HOM_0000020
database_cross_reference: homology method.html

in ohnology relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that results from a whole genome duplication event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: ohnologous to
has_related_synonym: homoeology

Axiom
annotated source: in ohnology relationship with
annotated property: definition
annotated target: Paralogy that results from a whole genome duplication event.
database_cross_reference: http://dx.doi.org/10.1038/75560
database_cross_reference: HOM_0000022

in in-paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
property disjoint with: in out-paralogy relationship with
definition: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: in-paralogous to
has_exact_synonym: inparalogy
has_exact_synonym: symparalogy

Axiom
annotated source: in in-paralogy relationship with
annotated property: definition
annotated target: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000023

in out-paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that results from a duplication preceding a given speciation event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: alloparalogy
has_exact_synonym: out-paralogous to
has_exact_synonym: outparalogy

Axiom
annotated source: in out-paralogy relationship with
annotated property: definition
annotated target: Paralogy that results from a duplication preceding a given speciation event.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000024

in pro-orthology relationship with
type: ObjectProperty
sub property of: in 1 to many orthology relationship with
type: SymmetricProperty
definition: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: pro-orthologous to

Axiom
annotated source: in pro-orthology relationship with
annotated property: definition
annotated target: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
database_cross_reference: scdb.1999.0338
database_cross_reference: nrg2099
database_cross_reference: HOM_0000025

in semi-orthology relationship with
type: ObjectProperty
sub property of: in 1 to many orthology relationship with
type: SymmetricProperty
definition: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: semi-orthologous to
comment: The converse of pro-orthologous.

Axiom
annotated source: in semi-orthology relationship with
annotated property: definition
annotated target: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
database_cross_reference: scdb.1999.0338
database_cross_reference: nrg2099
database_cross_reference: HOM_0000026

in serial homology relationship with
type: ObjectProperty
sub property of: in iterative homology relationship with
type: SymmetricProperty
definition: Iterative homology that involves structures arranged along the main body axis.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: serial homologous to
has_related_synonym: homonomy

Axiom
annotated source: in serial homology relationship with
annotated property: definition
annotated target: Iterative homology that involves structures arranged along the main body axis.
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000027

in heterochronous homology relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
definition: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: heterochronous homologous to
has_exact_synonym: heterochrony

Axiom
annotated source: in heterochronous homology relationship with
annotated property: definition
annotated target: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
database_cross_reference: HOM_0000028
database_cross_reference: ISBN:978-0674639416

in paedomorphorsis relationship with
type: ObjectProperty
sub property of: in heterochronous homology relationship with
type: SymmetricProperty
property disjoint with: in peramorphosis relationship with
definition: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: juvenification
has_exact_synonym: pedomorphosis

Axiom
annotated source: in paedomorphorsis relationship with
annotated property: definition
annotated target: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
database_cross_reference: Pedomorphosis
database_cross_reference: HOM_0000029
database_cross_reference: ISBN:978-0674639416

in peramorphosis relationship with
type: ObjectProperty
sub property of: in heterochronous homology relationship with
type: SymmetricProperty
definition: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in peramorphosis relationship with
annotated property: definition
annotated target: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
database_cross_reference: Peramorphosis
database_cross_reference: HOM_0000030

in progenesis relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
definition: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in progenesis relationship with
annotated property: definition
annotated target: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
database_cross_reference: Progenesis
database_cross_reference: HOM_0000031
database_cross_reference: ISBN:978-0674639416

in neoteny relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
definition: Paedomorphosis that is produced by a retardation of somatic development.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: juvenilization
has_exact_synonym: neotenous to

Axiom
annotated source: in neoteny relationship with
annotated property: definition
annotated target: Paedomorphosis that is produced by a retardation of somatic development.
database_cross_reference: Neoteny
database_cross_reference: HOM_0000032
database_cross_reference: ISBN:978-0674639416

in mimicry relationship with
type: ObjectProperty
sub property of: in convergence relationship with
type: SymmetricProperty
definition: Convergence that results from co-evolution usually involving an evolutionary arms race.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: mimicrous to

Axiom
annotated source: in mimicry relationship with
annotated property: definition
annotated target: Convergence that results from co-evolution usually involving an evolutionary arms race.
database_cross_reference: Mimicry
database_cross_reference: HOM_0000033

in 1 to many orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in 1 to many homology relationship with
type: SymmetricProperty
definition: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to many orthologous to
has_exact_synonym: 1:many orthology
has_exact_synonym: one-to-many orthology
has_related_synonym: co-orthology
has_related_synonym: many to 1 orthology

Axiom
annotated source: in 1 to many orthology relationship with
annotated property: definition
annotated target: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
database_cross_reference: 415741a
database_cross_reference: HOM_0000034
database_cross_reference: homology method.html

in many to many homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves two members of a larger set of homologs.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: many to many homologous to
has_exact_synonym: many-to-many homology
has_exact_synonym: many:many homology

Axiom
annotated source: in many to many homology relationship with
annotated property: definition
annotated target: Historical homology that involves two members of a larger set of homologs.
database_cross_reference: msp002
database_cross_reference: HOM_0000036

in 1 to many homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to many homologous to
has_exact_synonym: one-to-many homology
has_related_synonym: 1:many homology

Axiom
annotated source: in 1 to many homology relationship with
annotated property: definition
annotated target: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
database_cross_reference: HOM_0000037
database_cross_reference: BGEE:curator

in apomorphy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
property disjoint with: in plesiomorphy relationship with
definition: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: apomorphous to
has_related_synonym: synapomorphy

Axiom
annotated source: in apomorphy relationship with
annotated property: definition
annotated target: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
database_cross_reference: HOM_0000042
database_cross_reference: ISBN:978-0252068140

in plesiomorphy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that is based on distant shared ancestry.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: plesiomorphous to
has_related_synonym: symplesiomorphy
comment: This term is usually contrasted to apomorphy.

Axiom
annotated source: in plesiomorphy relationship with
annotated property: definition
annotated target: Historical homology that is based on distant shared ancestry.
database_cross_reference: HOM_0000043
database_cross_reference: ISBN:978-0252068140

in deep homology relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
sub property of: in parallelism relationship with
type: SymmetricProperty
definition: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: deep genetic homology
has_exact_synonym: deep homologous to
has_related_synonym: generative homology
has_related_synonym: homoiology
comment: Used for structures in distantly related taxa.

Axiom
annotated source: in deep homology relationship with
annotated property: definition
annotated target: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: nature07891
database_cross_reference: HOM_0000044

in hemiplasy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: hemiplasous to

Axiom
annotated source: in hemiplasy relationship with
annotated property: definition
annotated target: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
database_cross_reference: pnas.0807433105
database_cross_reference: HOM_0000045

in gametology relationship with
type: ObjectProperty
sub property of: in chromosomal homology relationship with
type: SymmetricProperty
definition: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: gametologous to

Axiom
annotated source: in gametology relationship with
annotated property: definition
annotated target: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
database_cross_reference: HOM_0000046
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/11110898

in chromosomal homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: MeSH:Chromosome_Pairing
has_exact_synonym: chromosomal homologous to

Axiom
annotated source: in chromosomal homology relationship with
annotated property: definition
annotated target: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
database_cross_reference: HOM_0000047
database_cross_reference: ISBN:0195307615

in many to many orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in many to many homology relationship with
type: SymmetricProperty
definition: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: many to many orthologous to
has_exact_synonym: many-to-many orthology
has_exact_synonym: many:many orthology
has_exact_synonym: trans-orthology
has_related_synonym: co-orthology
has_related_synonym: trans-homology

Axiom
annotated source: in many to many orthology relationship with
annotated property: definition
annotated target: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
database_cross_reference: 415741a
database_cross_reference: HOM_0000048
database_cross_reference: homology method.html

in within-species paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
property disjoint with: in between-species paralogy relationship with
definition: Paralogy that involves genes from the same species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: within-species paralogous to

Axiom
annotated source: in within-species paralogy relationship with
annotated property: definition
annotated target: Paralogy that involves genes from the same species.
database_cross_reference: HOM_0000049
database_cross_reference: homology method.html

in between-species paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that involves genes from different species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: between-species paralogous to
comment: The genes have diverged before a speciation event.

Axiom
annotated source: in between-species paralogy relationship with
annotated property: definition
annotated target: Paralogy that involves genes from different species.
database_cross_reference: HOM_0000050
database_cross_reference: homology method.html

in postdisplacement relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
definition: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: post-displacement

Axiom
annotated source: in postdisplacement relationship with
annotated property: definition
annotated target: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
database_cross_reference: Pedomorphosis
database_cross_reference: HOM_0000051

in hypermorphosis relationship with
type: ObjectProperty
sub property of: in peramorphosis relationship with
type: SymmetricProperty
definition: Peramorphosis that is produced by a delay in the offset of development.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in hypermorphosis relationship with
annotated property: definition
annotated target: Peramorphosis that is produced by a delay in the offset of development.
database_cross_reference: Peramorphosis
database_cross_reference: HOM_0000052
database_cross_reference: ISBN:978-0674639416

in synology relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
definition: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: synologous to

Axiom
annotated source: in synology relationship with
annotated property: definition
annotated target: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
database_cross_reference: http://dx.doi.org/10.1007/BF00173425
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000053

in isoorthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in equivalogy relationship with
type: SymmetricProperty
definition: Orthology that involves functional equivalent genes with retention of the ancestral function.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000080
has_exact_synonym: isoorthologous to

Axiom
annotated source: in isoorthology relationship with
annotated property: definition
annotated target: Orthology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000054

in tandem paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: tandem paralogous to
has_related_synonym: iterative paralogy
has_related_synonym: serial paralogy

Axiom
annotated source: in tandem paralogy relationship with
annotated property: definition
annotated target: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000055
database_cross_reference: ISBN:978-0878932665

in latent homology relationship with
type: ObjectProperty
sub property of: in parallelism relationship with
sub property of: in syngeny relationship with
type: SymmetricProperty
definition: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: apomorphic tendency
has_exact_synonym: cryptic homology
has_exact_synonym: latent homologous to
has_exact_synonym: underlying synapomorphy
has_related_synonym: homoiology
has_related_synonym: homoplastic tendency
has_related_synonym: re-awakening
comment: Used for structures in closely related taxa.

Axiom
annotated source: in latent homology relationship with
annotated property: definition
annotated target: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000057
database_cross_reference: ISBN:0199141118

in syngeny relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
type: SymmetricProperty
definition: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: generative homology
has_exact_synonym: syngenous to
comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.

Axiom
annotated source: in syngeny relationship with
annotated property: definition
annotated target: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000058
database_cross_reference: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R

in apparent orthology relationship with
type: ObjectProperty
sub property of: in 1 to 1 homology relationship with
sub property of: in between-species paralogy relationship with
type: SymmetricProperty
definition: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1:1 paralogy
has_exact_synonym: apparent 1:1 orthology
has_exact_synonym: apparent orthologous to
has_exact_synonym: pseudoorthology
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.

Axiom
annotated source: in apparent orthology relationship with
annotated property: definition
annotated target: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000060
database_cross_reference: homology method.html

in pseudoparalogy relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
definition: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: pseudoparalogous to
comment: These genes may come out as paralogs in a single-genome analysis.

Axiom
annotated source: in pseudoparalogy relationship with
annotated property: definition
annotated target: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000061

in equivalogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
sub property of: in functional equivalence relationship with
type: SymmetricProperty
definition: Historical homology that involves functional equivalent genes with retention of the ancestral function.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: equivalogous to
comment: This may include examples of orthology, paralogy and xenology.

Axiom
annotated source: in equivalogy relationship with
annotated property: definition
annotated target: Historical homology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: gkl1043
database_cross_reference: HOM_0000062

in interology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: interologous to

Axiom
annotated source: in interology relationship with
annotated property: definition
annotated target: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
database_cross_reference: gr.1774904
database_cross_reference: science.287.5450.116
database_cross_reference: HOM_0000063

in functional equivalence relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
definition: Similarity that is characterized by interchangeability in function.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: functional similarity

Axiom
annotated source: in functional equivalence relationship with
annotated property: definition
annotated target: Similarity that is characterized by interchangeability in function.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: 415741a
database_cross_reference: HOM_0000065

in iterative homology relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
definition: Biological homology that involves parts of the same organism.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: iterative homologous to

Axiom
annotated source: in iterative homology relationship with
annotated property: definition
annotated target: Biological homology that involves parts of the same organism.
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000066

in paraxenology relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
definition: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: duplicate xenology
has_exact_synonym: multiple xenology
has_exact_synonym: paraxenologous to

Axiom
annotated source: in paraxenology relationship with
annotated property: definition
annotated target: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
database_cross_reference: HOM_0000068
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in plerology relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: plerologous to
comment: This phenomenon is usually due to gene conversion process.

Axiom
annotated source: in plerology relationship with
annotated property: definition
annotated target: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
database_cross_reference: HOM_0000069
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in homotopy relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
property disjoint with: in homeosis relationship with
definition: Structural homology that involves structures with the same or similar relative positions.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homotopous to
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.

Axiom
annotated source: in homotopy relationship with
annotated property: definition
annotated target: Structural homology that involves structures with the same or similar relative positions.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: HOM_0000071
database_cross_reference: ISBN:0123195837

in homeosis relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
definition: Biological homology that involves an ectopic structure and the normally positioned structure.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: heterotopy

Axiom
annotated source: in homeosis relationship with
annotated property: definition
annotated target: Biological homology that involves an ectopic structure and the normally positioned structure.
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: j.cell.2008.06.030
database_cross_reference: HOM_0000072

in homoeology relationship with
type: ObjectProperty
sub property of: in ohnology relationship with
sub property of: in synology relationship with
type: SymmetricProperty
definition: Synology that results from allopolyploidy.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homoeologous to
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.

Axiom
annotated source: in homoeology relationship with
annotated property: definition
annotated target: Synology that results from allopolyploidy.
database_cross_reference: pnas.0505156102
database_cross_reference: HOM_0000073

in paramorphism relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
sub property of: in iterative homology relationship with
type: SymmetricProperty
definition: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: axis paramorphism

Axiom
annotated source: in paramorphism relationship with
annotated property: definition
annotated target: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
database_cross_reference: s10441-007-9023-8
database_cross_reference: j.1525-142x.2000.00054.x
database_cross_reference: HOM_0000074

in regulogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: regulogous to

Axiom
annotated source: in regulogy relationship with
annotated property: definition
annotated target: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
database_cross_reference: gr.1774904
database_cross_reference: HOM_0000075

has increased age-specific mortality rate
type: DatatypeProperty
range: Datatype
  on datatype: short
  with restrictions:
    min inclusive: 0
  with restrictions:
    max inclusive: 100
definition: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
created by: dos
creation date: 2018-05-22T16:43:28Z
comment: This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.

Axiom
annotated source: has increased age-specific mortality rate
annotated property: definition
annotated target: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
database_cross_reference: PMID:24138933
database_cross_reference: Wikipedia:Infant_mortality

continuant
type: Class
subclass of: Restriction
  on property: part of
  all values from: continuant
subclass of: Restriction
  on property: has prototype
  all values from: continuant
subclass of: Restriction
  on property: in similarity relationship with
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

occurrent
type: Class
subclass of: Restriction
  on property: part of
  all values from: occurrent
subclass of: Restriction
  on property: in similarity relationship with
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
definition: An entity that has temporal parts and that happens, unfolds or develops through time.

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

spatial region
type: Class
subclass of: immaterial entity

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has prototype
  all values from: process
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

disposition
type: Class
subclass of: realizable entity
disjoint with: role

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: realizable entity
disjoint with: quality
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: quality

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
disjoint with: generically dependent continuant
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.

role
type: Class
subclass of: realizable entity
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: generically dependent continuant
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity

anatomical entity
type: Class
subclass of: independent continuant
definition: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
id: CARO:0000000
comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
database_cross_reference: CAROC:Brownsville2014

connected anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
id: CARO:0000003
comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.

material anatomical entity
type: Class
subclass of: anatomical entity
disjoint with: immaterial anatomical entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial anatomical entity
definition: An anatomical entity that has mass.
id: CARO:0000006

immaterial anatomical entity
type: Class
subclass of: immaterial entity
subclass of: anatomical entity
disjoint with: Restriction
  on property: has part
  some values from: material anatomical entity
definition: Anatomical entity that has no mass.
id: CARO:0000007

neuron projection bundle
type: Class
subclass of: material anatomical entity
definition: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
id: CARO:0001001

organism or virus or viroid
type: Class
subclass of: material entity
definition: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
IAO_0000117: Melissa Haendel

multicellular anatomical structure
type: Class
subclass of: connected anatomical structure
definition: An anatomical structure that has more than one cell as a part.
IAO_0000117: djs93
id: CARO:0010000

cell
type: Class
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FBbt:00007002
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: MESH:D002477
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

Axiom
annotated source: cell
annotated property: definition
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: CARO:mah

sensory neuron
type: Class
subclass of: neuron
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
database_cross_reference: BTO:0001037
database_cross_reference: FBbt:00005124
database_cross_reference: FMA:84649
database_cross_reference: MESH:D011984
database_cross_reference: WBbt:0005759

Axiom
annotated source: sensory neuron
annotated property: definition
annotated target: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
database_cross_reference: ISBN:0721662544

neuron
type: Class
subclass of: material entity
subclass of: cell
definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000938
database_cross_reference: CALOHA:TS-0683
database_cross_reference: FBbt:00005106
database_cross_reference: FMA:54527
database_cross_reference: VHOG:0001483
database_cross_reference: WBbt:0003679
has_exact_synonym: nerve cell
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.

Axiom
annotated source: neuron
annotated property: definition
annotated target: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
database_cross_reference: MESH:D009474
database_cross_reference: http://en.wikipedia.org/wiki/Neuron

environmental system
type: Class
subclass of: system
definition: A system which has the disposition to environ one or more material entities.
creation date: 2013-09-23T16:04:08Z
database_cross_reference: EcoLexicon:environment
has_exact_synonym: environment
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.

Axiom
annotated source: environmental system
annotated property: definition
annotated target: A system which has the disposition to environ one or more material entities.
database_cross_reference: DOI:10.1186/2041-1480-4-43

molecular_function
type: Class
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
has_exact_synonym: molecular function
id: GO:0003674
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
database_cross_reference: GOC:pdt

ubiquitin-protein transferase activity
type: Class
subclass of: molecular_function
definition: Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
database_cross_reference: KEGG_REACTION:R03876
database_cross_reference: Reactome:R-HSA-1169394
database_cross_reference: Reactome:R-HSA-1169395
database_cross_reference: Reactome:R-HSA-1169397
database_cross_reference: Reactome:R-HSA-1169398
database_cross_reference: Reactome:R-HSA-1169402
database_cross_reference: Reactome:R-HSA-1169405
database_cross_reference: Reactome:R-HSA-1169406
database_cross_reference: Reactome:R-HSA-1234163
database_cross_reference: Reactome:R-HSA-1234172
database_cross_reference: Reactome:R-HSA-1253282
database_cross_reference: Reactome:R-HSA-1358789
database_cross_reference: Reactome:R-HSA-1358790
database_cross_reference: Reactome:R-HSA-1358792
database_cross_reference: Reactome:R-HSA-1363331
database_cross_reference: Reactome:R-HSA-168915
database_cross_reference: Reactome:R-HSA-173542
database_cross_reference: Reactome:R-HSA-173545
database_cross_reference: Reactome:R-HSA-174057
database_cross_reference: Reactome:R-HSA-174104
database_cross_reference: Reactome:R-HSA-174144
database_cross_reference: Reactome:R-HSA-174159
database_cross_reference: Reactome:R-HSA-174195
database_cross_reference: Reactome:R-HSA-174227
database_cross_reference: Reactome:R-HSA-179417
database_cross_reference: Reactome:R-HSA-180540
database_cross_reference: Reactome:R-HSA-180597
database_cross_reference: Reactome:R-HSA-182986
database_cross_reference: Reactome:R-HSA-182993
database_cross_reference: Reactome:R-HSA-183036
database_cross_reference: Reactome:R-HSA-183051
database_cross_reference: Reactome:R-HSA-183084
database_cross_reference: Reactome:R-HSA-183089
database_cross_reference: Reactome:R-HSA-1852623
database_cross_reference: Reactome:R-HSA-187575
database_cross_reference: Reactome:R-HSA-1912357
database_cross_reference: Reactome:R-HSA-1912386
database_cross_reference: Reactome:R-HSA-1918092
database_cross_reference: Reactome:R-HSA-1918095
database_cross_reference: Reactome:R-HSA-1977296
database_cross_reference: Reactome:R-HSA-1980074
database_cross_reference: Reactome:R-HSA-1980118
database_cross_reference: Reactome:R-HSA-201425
database_cross_reference: Reactome:R-HSA-202453
database_cross_reference: Reactome:R-HSA-202534
database_cross_reference: Reactome:R-HSA-205118
database_cross_reference: Reactome:R-HSA-209063
database_cross_reference: Reactome:R-HSA-211734
database_cross_reference: Reactome:R-HSA-2169050
database_cross_reference: Reactome:R-HSA-2172172
database_cross_reference: Reactome:R-HSA-2179276
database_cross_reference: Reactome:R-HSA-2186747
database_cross_reference: Reactome:R-HSA-2186785
database_cross_reference: Reactome:R-HSA-2187368
database_cross_reference: Reactome:R-HSA-2213017
database_cross_reference: Reactome:R-HSA-264444
database_cross_reference: Reactome:R-HSA-2682349
database_cross_reference: Reactome:R-HSA-2730904
database_cross_reference: Reactome:R-HSA-2737728
database_cross_reference: Reactome:R-HSA-2769007
database_cross_reference: Reactome:R-HSA-2900765
database_cross_reference: Reactome:R-HSA-3000335
database_cross_reference: Reactome:R-HSA-3134804
database_cross_reference: Reactome:R-HSA-3134946
database_cross_reference: Reactome:R-HSA-3249386
database_cross_reference: Reactome:R-HSA-3780995
database_cross_reference: Reactome:R-HSA-3781009
database_cross_reference: Reactome:R-HSA-3788724
database_cross_reference: Reactome:R-HSA-3797226
database_cross_reference: Reactome:R-HSA-400267
database_cross_reference: Reactome:R-HSA-4332236
database_cross_reference: Reactome:R-HSA-446877
database_cross_reference: Reactome:R-HSA-450358
database_cross_reference: Reactome:R-HSA-451418
database_cross_reference: Reactome:R-HSA-5205682
database_cross_reference: Reactome:R-HSA-5357757
database_cross_reference: Reactome:R-HSA-5362412

Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: definition
annotated target: Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
database_cross_reference: GOC:BioGRID
database_cross_reference: GOC:jh2
database_cross_reference: PMID:9635407

ISGylation of IRF3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169394

ISGylation of viral protein NS1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169395

Activation of ISG15 by UBA7 E1 ligase
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169397

ISGylation of host protein filamin B
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169398

ISGylation of E2 conjugating enzymes
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169402

ISGylation of protein phosphatase 1 beta (PP2CB)
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169405

ISGylation of host proteins
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1169406

Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1234163

Nuclear VBC complex ubiquitinylates HIF-alpha
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1234172

ERBB4 ubiquitination by WWP1/ITCH
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1253282

Self-ubiquitination of RNF41
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1358789

RNF41 ubiquitinates ERBB3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1358790

RNF41 ubiquitinates activated ERBB3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1358792

Ubiquitination of p130 (RBL2) by SCF (Skp2)
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1363331

K63-linked ubiquitination of RIP1 bound to the activated TLR complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-168915

SMURF2 ubiquitinates SMAD2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-173542

Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-173545

Multiubiquitination of APC/C-associated Cdh1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-174057

Ubiquitination of Cyclin A by APC/C:Cdc20 complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-174104

Ubiquitination of Securin by phospho-APC/C:Cdc20 complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-174144

Ubiquitination of Emi1 by SCF-beta-TrCP
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-174159

Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-174195

Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-174227

Multiubiquitination of Nek2A
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-179417

Multi-ubiquitination of APOBEC3G
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-180540

Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-180597

CBL-mediated ubiquitination of CIN85
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-182986

Ubiquitination of stimulated EGFR (CBL)
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-182993

Ubiquitination of stimulated EGFR (CBL:GRB2)
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-183036

CBL ubiquitinates Sprouty
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-183051

CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-183084

CBL binds and ubiquitinates phosphorylated Sprouty
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-183089

Ubiquitination of NICD1 by FBWX7
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1852623

Ubiquitination of phospho-p27/p21
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-187575

ITCH ubiquitinates DTX
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1912357

Ubiquitination of NOTCH1 by ITCH in the absence of ligand
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1912386

CHIP (STUB1) mediates ubiquitination of ERBB2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1918092

CUL5 mediates ubiquitination of ERBB2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1918095

NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1977296

Ubiquitination of DLL/JAG ligands upon binding to NOTCH1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1980074

ARRB mediates NOTCH1 ubiquitination
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1980118

Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-201425

Auto-ubiquitination of TRAF6
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-202453

Ubiquitination of NEMO by TRAF6
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-202534

TRAF6 polyubiquitinates NRIF
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-205118

Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-209063

Ubiquitination of PAK-2p34
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211734

SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2169050

Ubiquitination of DLL/JAG ligands upon binding to NOTCH2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2172172

SMURF2 monoubiquitinates SMAD3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2179276

Ubiquitination of SKI/SKIL by RNF111/SMURF2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2186747

RNF111 ubiquitinates SMAD7
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2186785

STUB1 (CHIP) ubiquitinates SMAD3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2187368

Auto-ubiquitination of TRAF3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2213017

Autoubiquitination of phospho-COP1(Ser-387 )
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-264444

RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2682349

Auto-ubiquitination of TRAF6
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2730904

Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2737728

Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2769007

Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2900765

SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3000335

STING ubiquitination by TRIM32 or TRIM56
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3134804

DDX41 ubiquitination by TRIM21
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3134946

DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3249386

NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3780995

NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3781009

Cdh1:APC/C ubiquitinates EHMT1 and EHMT2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3788724

Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3797226

BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-400267

CBL neddylates TGFBR2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-4332236

TRAF6 is K63 poly-ubiquitinated
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-446877

Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-450358

Pellino ubiquitinates IRAK1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-451418

Parkin promotes the ubiquitination of mitochondrial substrates
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5205682

BIRC(cIAP1/2) ubiquitinates RIPK1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5357757

SYVN1 ubiquitinates Hh C-terminal fragments
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5362412

Hh processing variants are ubiquitinated
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5483238

SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5607725

beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5607728

TRAF6 oligomer autoubiquitinates
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5607756

K63polyUb-TRAF6 ubiquitinates TAK1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5607757

SCF(beta-TrCP) ubiquitinates p-GLI1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5610742

SCF(beta-TrCP) ubiquitinates p-GLI2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5610745

SCF(beta-TrCP) ubiquitinates p-GLI3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5610746

RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5652009

RCHY1 monoubiquitinates POLH
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5655170

SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5660753

SIAH1, SIAH2 ubiquitinate SNCAIP
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5667107

PARK2 K63-Ubiquitinates SNCAIP
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5667111

K63polyUb-cIAP1,2 ubiquitinates TRAF3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5668454

cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5668534

BIRC2/3 (cIAP1/2) is autoubiquitinated
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5675470

SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5684250

SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5691108

TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5693108

Ubiquitination of phosphorylated Cdc25A
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-69598

RIP2 induces K63-linked ubiquitination of NEMO
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-741386

Ubiquitination of Cyclin D1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-75824

TRIM33 monoubiquitinates SMAD4
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-870449

DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8948709

VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8956106

Ubiquitination of DLL/JAG ligands upon binding to NOTCH3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9013069

Auto-ubiquitination of TRAF3 within activated TLR3 complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9013974

K63-linked ubiquitination of RIP1 bound to the activated TLR complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9014342

DDX58 is K63 polyubiquitinated
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-918224

RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-936412

Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-936942

Activated TRAF6 synthesizes unanchored polyubiquitin chains
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-936986

Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9628444

Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9645394

Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9645414

STUB1 ubiquitinates RIPK3 at K55, K363
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9688831

BRCA1:BARD1 heterodimer autoubiquitinates
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9701000

TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-975118

Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-975147

Transfer of Ub from E2 to substrate and release of E2
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-983140

E1 mediated ubiquitin activation
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-983153

Polyubiquitination of substrate
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-983156

Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: has_narrow_synonym
annotated target: anaphase-promoting complex activity
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

nucleus
type: Class
definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
database_cross_reference: NIF_Subcellular:sao1702920020
database_cross_reference: Wikipedia:Cell_nucleus
has_exact_synonym: cell nucleus
has_narrow_synonym: horsetail nucleus
id: GO:0005634

Axiom
annotated source: nucleus
annotated property: definition
annotated target: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
database_cross_reference: GOC:go_curators

Axiom
annotated source: nucleus
annotated property: has_narrow_synonym
annotated target: horsetail nucleus
database_cross_reference: GOC:al
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw
database_cross_reference: PMID:15030757

biological_process
type: Class
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
created by: jl
creation date: 2012-09-19T15:05:24Z
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
database_cross_reference: GOC:pdt

kinase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: Reactome:R-HSA-6788855
database_cross_reference: Reactome:R-HSA-6788867
has_exact_synonym: phosphokinase activity
id: GO:0016301
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788867

myristoyltransferase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is myristoyltransferase activity
  has self: true
definition: Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
database_cross_reference: Reactome:R-HSA-141367
database_cross_reference: Reactome:R-HSA-162914
id: GO:0019107

Axiom
annotated source: myristoyltransferase activity
annotated property: definition
annotated target: Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
database_cross_reference: GOC:ai

Myristoylation of tBID by NMT1
type: Axiom
annotated source: myristoyltransferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-141367

Myristoylation of Nef
type: Axiom
annotated source: myristoyltransferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-162914

disease
type: Class
subclass of: disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
database_cross_reference: PATOC:GVG

branched
type: Class
subclass of: quality
definition: A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
is opposite of: PATO_0000414
has_exact_synonym: ramified
has_exact_synonym: ramiform
id: PATO:0000402

Axiom
annotated source: branched
annotated property: definition
annotated target: A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
database_cross_reference: WordNet:WordNet

linear
type: Class
subclass of: quality
definition: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
id: PATO:0001199

Axiom
annotated source: linear
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
database_cross_reference: ISBN:0881923214

laminar
type: Class
subclass of: quality
definition: A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
contributor: 0000-0002-2061-091X
creation date: 2009-10-06T04:37:14Z
id: PATO:0002124

Axiom
annotated source: laminar
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
database_cross_reference: PATOC:GVG

exposure event or process
type: Class
subclass of: process
IAO_0000112: An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
IAO_0000112: An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
definition: A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
IAO_0000116: This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
creator: https://orcid.org/0000-0002-6601-2165
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-06-05T17:55:39Z

sequentially ordered entity
type: Class
subclass of: Restriction
  on property: has subsequence
  some values from: sequence atomic unit
definition: Any entity that is ordered in discrete units along a linear axis.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

sequence atomic unit
type: Class
subclass of: sequentially ordered entity
definition: Any individual unit of a collection of like units arranged in a linear order
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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.

sequence bearer
type: Class
subclass of: sequentially ordered entity
definition: Any entity that can be divided into parts such that each part is an atomical unit of a sequence
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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: material entity
definition: A material entity consisting of multiple components that are causally integrated.
IAO_0000116: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.jbiomedsem.com/content/4/1/43

phenotype
type: Class
subclass of: quality

axiom holds for all times
type: NamedIndividual
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

relation has no temporal argument
type: NamedIndividual
definition: ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)

curation status specification
IAO_0000114: pending final vetting

ready for release
IAO_0000114: pending final vetting

obsolescence reason specification
IAO_0000114: pending final vetting

requires discussion
IAO_0000114: pending final vetting

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y

Restriction
on property: is ubiquitination
has self: true