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: 2024-02-13

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred term: example of usage
has curation status: ready for release
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: ready for release
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: ready for release
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred term: alternative label
has curation status: pending final vetting
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: ready for release
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred term: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

imported from
type: AnnotationProperty
editor preferred term: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
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.
term editor: PERSON:Alan Ruttenberg
sub property of: logical macro assertion on an object property

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

elucidation
type: AnnotationProperty
editor preferred term: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has ontology root term
type: AnnotationProperty
editor preferred term: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
has curation status: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

defined by construct
type: AnnotationProperty
example of usage: '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.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: James P. Balhoff

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
example of usage: 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.
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947
expand assertion to: 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.
alternative label: non-overlapping with
alternative label: shares no parts with
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
expand assertion to: 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.
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
definition source: 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
editor note: 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
example of usage: '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.
alternative label: shares no connection with
expand assertion to: 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
example of usage: brain always_present_in_taxon 'Vertebrata'
example of usage: 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
editor note: 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.
alternative label: never lost in
sub property of: present in taxon

temporal logical macro assertion on a class
type: AnnotationProperty
curator note: 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.
curator note: 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
editor note: 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: Christopher J. Mungall
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: Christopher J. Mungall
sub property of: logical macro assertion on an object property

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

is a defining property chain axiom
type: AnnotationProperty
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
curator note: 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
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: '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
curator note: 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
curator note: 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
example of usage: 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.
curator note: 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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: Christopher J. Mungall
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

is homeomorphic for
type: AnnotationProperty
example of usage: 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: Christopher J. Mungall
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: Pascale Gaudet
creation date: 2020-09-22T11:05:29Z
sub property of: subset_property

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

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

valid_for_gocam
type: AnnotationProperty
created by: Pascale Gaudet
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
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
label: has broad synonym
sub property of: alternative label

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
label: has exact synonym
sub property of: alternative label

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
label: has narrow synonym
sub property of: alternative label

has_obo_format_version
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
label: has related synonym
sub property of: alternative label

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
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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/
editor note: 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'.
alternative label: 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
is homeomorphic for: quality
is homeomorphic for: characteristic
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
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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/
editor note: 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'.
alternative label: 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
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [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
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: 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
editor preferred term: 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.
editor note: 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.
alternative label: is preceded by
alternative label: 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
editor preferred term: 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
domain: process
range: independent continuant
property chain axiom: part of
editor preferred term: 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
alternative label: occurs_in
alternative label: unfolds in
alternative label: 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
editor preferred term: 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
editor preferred term: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: 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.
alternative label: 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: characteristic
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
editor note: 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.
alternative label: bearer_of
alternative label: is bearer of
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: 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
alternative label: participates_in

has participant
type: ObjectProperty
domain: occurrent
domain: process
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: 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
editor note: 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.
alternative label: 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: characteristic
example of usage: 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).
example of usage: 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: characteristic
range: generically dependent continuant
example of usage: 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).
example of usage: 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
example of usage: 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
editor note: 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.
alternative label: function_of
alternative label: 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
example of usage: 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
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: 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
example of usage: 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
editor note: 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.
alternative label: is role of
alternative label: 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
example of usage: 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
editor note: 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.
alternative label: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
example of usage: 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
editor note: 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.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
example of usage: 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
editor note: 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.
alternative label: 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
has curation status: 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.
term editor: David Osumi-Sutherland
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
has curation status: 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.
term editor: David Osumi-Sutherland
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
has curation status: 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.
term editor: David Osumi-Sutherland
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
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: 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
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative label: derives_from
curator note: 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
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: 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
editor note: 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'.
alternative label: derives_into
in_subset: eco subset

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred term: is location of
example of usage: my head is the location of my brain
example of usage: 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
editor note: 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/
alternative label: location_of
temporal interpretation: axiom holds for all times

obsolete contained in
type: ObjectProperty
editor preferred term: contained in
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
editor note: 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):
alternative label: contained_in
deprecated: true

obsolete contains
type: ObjectProperty
editor preferred term: contains
deprecated: true

is allergic trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has allergic trigger
domain: material entity
example of usage: 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
example of usage: 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
editor preferred term: located in
example of usage: my brain is located in my head
example of usage: 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
editor note: 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
editor note: 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/
alternative label: 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
editor note: 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
editor note: 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
example of usage: 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
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: 2D_boundary_of
alternative label: boundary of
alternative label: is 2D boundary of
alternative label: is boundary of
alternative label: surface of
temporal interpretation: axiom holds for all times

aligned with
type: ObjectProperty
type: TransitiveProperty
has curation status: pending final vetting
editor note: May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
term editor: David Osumi-Sutherland
temporal interpretation: axiom holds for all times

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: immaterial entity
example of usage: 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
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
term editor: David Osumi-Sutherland
alternative label: has boundary
alternative label: 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.
term editor: David Osumi-Sutherland
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

tracheates
type: ObjectProperty
sub property of: located in
domain: anatomical structure
range: 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).
term editor: David Osumi-Sutherland

innervated_by
type: ObjectProperty
inverse of: innervates
domain: anatomical structure
range: neuron projection bundle
term editor: David Osumi-Sutherland
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
term editor: David Osumi-Sutherland
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
term editor: David Osumi-Sutherland
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.
editor note: Note from NCEAS meeting: consider changing primary label
term editor: David Osumi-Sutherland
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.
term editor: David Osumi-Sutherland
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 another 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).
term editor: David Osumi-Sutherland
has_exact_synonym: regulates in other organism
in_subset: valid_for_go_ontology

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.
term editor: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
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: David Osumi-Sutherland
creation date: 2017-07-20T17:19:37Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: David Osumi-Sutherland
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: David Osumi-Sutherland

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: David Osumi-Sutherland
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: David Osumi-Sutherland

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: David Osumi-Sutherland
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: David Osumi-Sutherland

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: David Osumi-Sutherland
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: David Osumi-Sutherland

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: David Osumi-Sutherland
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: David Osumi-Sutherland

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

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: SymmetricProperty
type: TransitiveProperty
definition: x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.
term editor: 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
term editor: 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
term editor: 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
term editor: David Osumi-Sutherland
alternative label: 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
term editor: 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
term editor: David Osumi-Sutherland
alternative label: 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
term editor: 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
term editor: 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
term editor: David Osumi-Sutherland
alternative label: ends_at_start_of
alternative label: 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
term editor: David Osumi-Sutherland
alternative label: 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
term editor: David Osumi-Sutherland
alternative label: d
alternative label: 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
term editor: David Osumi-Sutherland
alternative label: o
alternative label: 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: material anatomical entity
property chain axiom: part of
has curation status: pending final vetting
definition: Relation between a neuron and a material anatomical entity that its soma is part of.
term editor: David Osumi-Sutherland
expand expression to: <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
has curation status: 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.
term editor: David Osumi-Sutherland
alternative label: fasciculates with
first order logic expression: (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
has curation status: pending final vetting
definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
expand expression to: <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
has curation status: pending final vetting
definition: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
expand expression to: <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
example of usage: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
has curation status: 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.
term editor: https://orcid.org/0000-0001-9990-8331
term editor: Christopher J. Mungall
term editor: Lindsay G Cowell
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19243617
expand expression to: <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
has curation status: pending final vetting
definition: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: David Osumi-Sutherland
expand expression to: 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
has curation status: pending final vetting
definition: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: David Osumi-Sutherland
expand expression to: 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
has curation status: pending final vetting
definition: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: David Osumi-Sutherland
expand expression to: 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
has curation status: pending final vetting
definition: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: David Osumi-Sutherland
expand expression to: 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
has curation status: pending final vetting
definition: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: David Osumi-Sutherland
expand expression to: 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
has curation status: pending final vetting
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
alternative label: synapsed in
expand expression to: 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: anatomical structure
range: material entity
has curation status: pending final vetting
alternative label: has neurotransmitter

synapsed_by_via_type_Is_bouton
type: ObjectProperty
sub property of: synapsed by
has curation status: pending final vetting
definition: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: David Osumi-Sutherland
expand expression to: 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
has curation status: pending final vetting
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
alternative label: synapses in
expand expression to: <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.
expand expression to: 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.
expand expression to: 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
has curation status: pending final vetting
definition: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
expand expression to: <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
has curation status: pending final vetting
definition: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
expand expression to: <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
has curation status: 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.
term editor: David Osumi-Sutherland
alternative label: has synapse in
expand expression to: <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
has curation status: 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
expand expression to: 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
has curation status: pending final vetting
definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
term editor: David Osumi-Sutherland
alternative label: has fasciculating component
first order logic expression: (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
has curation status: 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.
term editor: David Osumi-Sutherland
expand expression to: <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
has curation status: pending final vetting
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
term editor: David Osumi-Sutherland
alternative label: connected to
curator note: 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
has curation status: 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
editor note: 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
alternative label: proper overlaps
first order logic expression: (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
has curation status: 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.
alternative label: ancestral_stucture_of
alternative label: evolutionarily_descended_from

has derived by descendant
type: ObjectProperty
sub property of: evolutionarily related to
type: TransitiveProperty
has curation status: 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
has curation status: 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.
curator note: 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
has curation status: pending final vetting

only in taxon
type: ObjectProperty
sub property of: in taxon
example of usage: lactation SubClassOf 'only in taxon' some 'Mammalia'
has curation status: 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.
editor note: 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
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: organism
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
has curation status: 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.
term editor: 0000-0001-9227-417X
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: 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
has curation status: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: 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.
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: 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
expand expression to: 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
example of usage: 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
definition source: 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
example of usage: The M8 connects Glasgow and Edinburgh
example of usage: 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.
definition source: 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: anatomical structure
range: 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.
editor note: 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
definition source: 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.
editor note: 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
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
sub property of: has part
has curation status: 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.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: 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: disease
  union of: material anatomical entity
range: phenotype
has curation status: 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).
term editor: Christopher J. Mungall
in_subset: eco subset

phenotype of
type: ObjectProperty
type: FunctionalProperty
has curation status: pending final vetting
definition: inverse of has phenotype
term editor: Christopher J. Mungall
in_subset: defined by inverse
in_subset: eco subset

develops from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
has curation status: 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
term editor: https://orcid.org/0000-0001-9114-8737
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
term editor: 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
has curation status: pending final vetting
definition: inverse of develops from
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
term editor: 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
has curation status: 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"
editor note: 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.
term editor: Christopher J. Mungall

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
example of usage: every HOTAIR lncRNA is the gene product of some HOXC gene
example of usage: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
has curation status: 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
term editor: Christopher J. Mungall

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
example of usage: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
has curation status: 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
term editor: Christopher J. Mungall

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
domain: Class
  union of: cell
  union of: multicellular anatomical structure
range: Class
  union of: cell
  union of: multicellular anatomical structure
has curation status: 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.
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
definition source: 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
has curation status: pending final vetting
definition: inverse of directly develops from
alternative label: 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.
term editor: https://orcid.org/0000-0001-7476-6306
term editor: https://orcid.org/0000-0002-3837-8864
term editor: Christopher J. Mungall
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
elucidation: 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.
term editor: Christopher J. Mungall
definition source: 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.
term editor: Christopher J. Mungall
definition source: 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
example of usage: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
has curation status: 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.
editor note: 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)
editor note: TODO: add homeomorphy axiom
editor note: 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.
term editor: Christopher J. Mungall

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: 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.
term editor: Christopher J. Mungall
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: 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.
term editor: Christopher J. Mungall
alternative label: 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
term editor: Christopher J. Mungall
alternative label: 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
term editor: Christopher J. Mungall
alternative label: has agent
term replaced by: causal agent in process
deprecated: true

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
has curation status: 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
term editor: Christopher J. Mungall
temporal interpretation: axiom holds for all times

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
example of usage: 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.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: 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.
has curation status: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
term editor: Christopher J. Mungall
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: example of usage
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
has curation status: pending final vetting
definition: inverse of surrounded by
term editor: Christopher J. Mungall
temporal interpretation: axiom holds for all times
in_subset: defined by inverse

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
term editor: Christopher J. Mungall
definition source: Allen's interval algebra
curator note: 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
has curation status: pending final vetting
definition: inverse of starts with
term editor: Christopher J. Mungall
term editor: Chris Mungall
definition source: Allen
in_subset: eco subset

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: 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.
term editor: Christopher J. Mungall
term editor: Chris Mungall
alternative label: 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
has curation status: 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
term editor: Christopher J. Mungall

develops in
type: ObjectProperty
sub property of: developmentally preceded by
domain: anatomical entity
property chain axiom: directly develops from
property chain axiom: located in
has curation status: pending final vetting
definition: x develops_in y if x is located in y whilst x is developing
term editor: Christopher J. Mungall
definition source: EHDAA2
definition source: 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
has curation status: pending final vetting
definition: inverse of ends with
term editor: Christopher J. Mungall
term editor: Chris Mungall
in_subset: eco subset

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
has curation status: 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.
term editor: Christopher J. Mungall
term editor: Chris Mungall
alternative label: 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
has curation status: 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
term editor: Christopher J. Mungall
alternative label: 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
has curation status: 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
term editor: Christopher J. Mungall
alternative label: 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
has curation status: 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.
term editor: Christopher J. Mungall
alternative label: 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
has curation status: 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.
term editor: Christopher J. Mungall
alternative label: 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.
term editor: https://orcid.org/0000-0001-9625-1899
curator note: 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.
definition source: 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.
definition source: 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
definition source: 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.
definition source: http://purl.obolibrary.org/obo/ExO_0000004

related via exposure to
type: ObjectProperty
sub property of: causally related to
domain: exposure of organism
definition: Any relationship between an exposure event or process and any other entity.
curator note: 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
example of usage: 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
example of usage: 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
example of usage: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
has curation status: pending final vetting
definition: x has developmental contribution from y iff x has some part z such that z develops from y
term editor: Christopher J. Mungall

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
has curation status: pending final vetting
definition: inverse of has developmental contribution from
term editor: Christopher J. Mungall
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
has curation status: 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
term editor: https://orcid.org/0000-0001-9114-8737
term editor: Christopher J. Mungall
term editor: David Osumi-Sutherland
alternative label: induced by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
definition source: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
definition source: GO:0001759
curator note: 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
has curation status: pending final vetting
definition: Inverse of developmentally induced by
term editor: Christopher J. Mungall

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
has curation status: 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
editor note: false
term editor: Christopher J. Mungall
curator note: 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
example of usage: 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
example of usage: 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
has curation status: 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
editor note: 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
term editor: Christopher J. Mungall
alternative label: replaces

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: pending final vetting
definition: Inverse of developmentally preceded by
term editor: Christopher J. Mungall

part of developmental precursor of
type: ObjectProperty
sub property of: developmentally succeeded by
property chain axiom: part of
property chain axiom: directly develops into
example of usage: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
has curation status: pending final vetting
term editor: Christopher J. Mungall

ubiquitously expressed in
type: ObjectProperty
sub property of: expressed in
inverse of: ubiquitously expresses
has curation status: 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
editor note: 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.
term editor: Christopher J. Mungall

expresses
type: ObjectProperty
sub property of: genomically related to
has curation status: pending final vetting
definition: y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
term editor: Christopher J. Mungall

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
has curation status: pending final vetting
definition: inverse of ubiquiotously expressed in
term editor: Christopher J. Mungall
in_subset: defined by inverse

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: biological_process
range: anatomical entity
has curation status: 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).
editor note: 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.
term editor: Christopher J. Mungall

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
example of usage: every flower development (GO:0009908) results in development of some flower (PO:0009046)
has curation status: 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.
term editor: Christopher J. Mungall
definition source: 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 anatomical entity
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
example of usage: 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.
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
has curation status: pending final vetting
term editor: Christopher J. Mungall
definition source: 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
example of usage: 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.
example of usage: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
has curation status: 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.
term editor: Christopher J. Mungall
definition source: 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
example of usage: 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
example of usage: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
has curation status: 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.
term editor: Christopher J. Mungall
definition source: 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
example of usage: foramen ovale closure SubClassOf results in disappearance of foramen ovale
has curation status: pending final vetting
term editor: Christopher J. Mungall
curator note: May be merged into parent relation

results in developmental regression of
type: ObjectProperty
sub property of: results in ending of
example of usage: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
has curation status: pending final vetting
term editor: Christopher J. Mungall
curator note: 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: Christopher J. Mungall
in_subset: defined by inverse

has habitat
type: ObjectProperty
sub property of: ecologically related to
domain: organism
range: environmental system
example of usage: 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
has curation status: 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.
term editor: Pier Luigi Buttigieg
alternative label: 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: Christopher J. Mungall
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: Christopher J. Mungall
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: Austin Meier
contributor: Christopher J. Mungall
contributor: Marie-Angélique Laporte
created by: Christopher J. Mungall
creation date: 2017-06-05T17:35:04Z

evolutionary variant of
type: ObjectProperty
sub property of: evolutionarily related to
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
alternative label: 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.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: Christopher J. Mungall
alternative label: inheres in part of
definition source: 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: anatomical structure
example of usage: 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
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
curator note: 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)
editor note: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
term editor: Christopher J. Mungall
curator note: 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
editor note: 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.
term editor: Christopher J. Mungall
alternative label: adapted for
in_subset: eco subset

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: Christopher J. Mungall
curator note: 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)
term editor: Christopher J. Mungall
curator note: 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
example of usage: 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].
term editor: Christopher J. Mungall
curator note: 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
example of usage: 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.
example of usage: 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.
example of usage: 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
editor note: 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.
term editor: Christopher J. Mungall
curator note: 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
example of usage: 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.
term editor: Christopher J. Mungall
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing
curator note: 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.
term editor: Christopher J. Mungall
curator note: 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.
term editor: Christopher J. Mungall
alternative label: 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.
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
alternative label: actively involved in
alternative label: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: process
range: material entity
example of usage: 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
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
in_subset: defined by inverse

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
curator note: 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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
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
example of usage: 'pollen tube growth' results_in growth_of some 'pollen tube'
term editor: Christopher J. Mungall

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to
example of usage: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
in_subset: valid_for_go_ontology

results in commitment to
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
example of usage: 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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
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
example of usage: 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.
alternative label: is member of
alternative label: member part of
definition source: 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.
definition source: 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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
in_subset: defined by inverse
in_subset: eco subset

formed as result of
type: ObjectProperty
sub property of: output of
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall

has dendrite location
type: ObjectProperty
sub property of: overlaps
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
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: 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.
term editor: Christopher J. Mungall
definition source: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle origin
annotated property: domain
annotated target: 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: 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.
term editor: Christopher J. Mungall
definition source: Wikipedia:Insertion_(anatomy)

Axiom
annotated source: has muscle insertion
annotated property: domain
annotated target: anatomical structure
editor note: 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
example of usage: false
has curation status: 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
term editor: Christopher J. Mungall
definition source: 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
has curation status: 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.
term editor: Christopher J. Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
curator note: 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
example of usage: Deschutes River tributary_of Columbia River
example of usage: inferior epigastric vein tributary_of external iliac vein
has curation status: 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.
term editor: Christopher J. Mungall
alternative label: drains into
alternative label: drains to
alternative label: tributary channel of
definition source: http://en.wikipedia.org/wiki/Tributary
definition source: http://www.medindia.net/glossary/venous_tributary.htm
curator note: 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
example of usage: Deschutes River distributary_of Little Lava Lake
has curation status: 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
term editor: Christopher J. Mungall
alternative label: branch of
alternative label: distributary channel of
definition source: 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
has curation status: 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.
term editor: Christopher J. Mungall
alternative label: 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
example of usage: A lump of clay and a statue
definition: x spatially_coextensive_with y if and inly if x and y have the same location
term editor: Christopher J. Mungall
curator note: 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
example of usage: 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
term editor: Christopher J. Mungall
in_subset: eco subset

main stem of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
example of usage: 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'.
has curation status: 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.
term editor: Christopher J. Mungall
in_subset: eco subset

proper distributary of
type: ObjectProperty
sub property of: distributary of
has curation status: requires discussion
definition: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
term editor: Christopher J. Mungall
in_subset: eco subset

proper tributary of
type: ObjectProperty
sub property of: tributary of
has curation status: requires discussion
definition: x proper_tributary_of y iff x tributary_of y and x does not originate from y
term editor: Christopher J. Mungall
in_subset: eco subset

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
has curation status: 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).
term editor: Christopher J. Mungall

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: 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
term editor: Christopher J. Mungall

has potential to developmentally induce
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: requires discussion
definition: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
term editor: Christopher J. Mungall

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: 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
term editor: Christopher J. Mungall

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
has curation status: 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
term editor: Christopher J. Mungall

has direct input
type: ObjectProperty
sub property of: has input
property chain axiom: starts with
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
has curation status: 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.
term editor: Christopher J. Mungall
alternative label: directly consumes
curator note: 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
has curation status: requires discussion
term editor: Christopher J. Mungall
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
example of usage: translation SubClassOf has_direct_output some protein
has curation status: 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.
term editor: Christopher J. Mungall
alternative label: directly produces
deprecated: true

obsolete has indirect output
type: ObjectProperty
property chain axiom: causally upstream of
property chain axiom: obsolete has direct output
has curation status: requires discussion
term editor: Christopher J. Mungall
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
has curation status: requires discussion
definition: inverse of upstream of
term editor: Christopher J. Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
alternative label: 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.
term editor: Christopher J. Mungall
alternative label: 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.
editor note: 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…
term editor: Christopher J. Mungall
curator note: 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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
alternative label: directly provides input for
definition source: 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
has curation status: requires discussion
definition: transitive form of directly_provides_input_for
term editor: Christopher J. Mungall
curator note: 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.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: Christopher J. Mungall
alternative label: influences (processual)
has_related_synonym: affects

differs in
type: ObjectProperty
editor note: false
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall

differs in attribute
type: ObjectProperty
sub property of: differs in
range: characteristic
term editor: Christopher J. Mungall

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall

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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
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
editor note: OWL does not allow defining object properties via a Union
term editor: Christopher J. Mungall
alternative label: 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
example of usage: 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.
term editor: Christopher J. Mungall
alternative label: 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: Christopher J. Mungall
database_cross_reference: David Osumi-Sutherland

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.
term editor: Christopher J. Mungall

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.
editor note: 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.
editor note: Considering relabeling as 'pairwise interacts with'
term editor: Christopher J. Mungall
curator note: 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
editor note: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
alternative label: binds
alternative label: 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.
term editor: Christopher J. Mungall
alternative label: 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.
term editor: Christopher J. Mungall
in_subset: eco subset

preys on
type: ObjectProperty
sub property of: trophically interacts with
inverse of: preyed upon by
example of usage: A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
example of usage: 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
term editor: https://orcid.org/0000-0001-7134-3324
term editor: Christopher J. Mungall
term editor: Jorrit Poelen
alternative label: is subject of predation interaction with
alternative label: 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.
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19278549
curator note: 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).
term editor: Christopher J. Mungall
definition source: 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).
term editor: Christopher J. Mungall
definition source: 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).
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19278549
curator note: 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
example of usage: Pediculus humanus capitis parasite of human
term editor: Christopher J. Mungall
alternative label: 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
term editor: Christopher J. Mungall
alternative label: has parasite
alternative label: 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
example of usage: 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.
term editor: Christopher J. Mungall
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
editor note: Axiomatization to GO to be added later
term editor: Christopher J. Mungall
alternative label: 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.
term editor: Christopher J. Mungall
term editor: 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.
term editor: Christopher J. Mungall
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: 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.
term editor: Christopher J. Mungall
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly activates
has_exact_synonym: molecularly increases activity of

transmitted by
type: ObjectProperty
sub property of: ecologically related to
example of usage: all dengue disease transmitted by some mosquito
definition: A relationship that holds between a disease and organism
editor note: Add domain and range constraints
term editor: Christopher J. Mungall

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
term editor: Christopher J. Mungall

host of
type: ObjectProperty
sub property of: symbiotically interacts with
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
in_subset: eco subset

pollinates
type: ObjectProperty
sub property of: mutualistically interacts with
inverse of: pollinated by
example of usage: Bees pollinate Flowers
editor note: 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.
term editor: Christopher J. Mungall
alternative label: is subject of pollination interaction with
in_subset: eco subset

pollinated by
type: ObjectProperty
sub property of: mutualistically interacts with
term editor: Christopher J. Mungall
alternative label: has polinator
alternative label: 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
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
alternative label: has predator
alternative label: 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
example of usage: Anopheles is a vector for Plasmodium
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
in_subset: eco subset

partner in
type: ObjectProperty
sub property of: participates in
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall

is commensalism
type: ObjectProperty
sub property of: is symbiosis
term editor: Christopher J. Mungall

is mutualism
type: ObjectProperty
sub property of: is symbiosis
term editor: Christopher J. Mungall

is parasitism
type: ObjectProperty
sub property of: is symbiosis
term editor: Christopher J. Mungall

provides nutrients for
type: ObjectProperty
sub property of: trophically interacts with
term editor: Christopher J. Mungall
in_subset: eco subset

eats
type: ObjectProperty
sub property of: trophically interacts with
term editor: Christopher J. Mungall
alternative label: is subject of eating interaction with
in_subset: eco subset

is eaten by
type: ObjectProperty
sub property of: trophically interacts with
term editor: Christopher J. Mungall
alternative label: eaten by
alternative label: 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.
term editor: Christopher J. Mungall
in_subset: eco subset

composed primarily of
type: ObjectProperty
sub property of: has part
domain: material entity
range: material entity
example of usage: '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.
term editor: Christopher J. Mungall
definition source: 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
example of usage: 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
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall

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
term editor: Christopher J. Mungall

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.
term editor: Christopher J. Mungall
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
editor note: Axiomatization to GO to be added later
term editor: Christopher J. Mungall

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
term editor: Christopher J. Mungall

is ubiquitination
type: ObjectProperty
sub property of: molecular interaction relation helper property
term editor: Christopher J. Mungall

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
editor note: See notes for inverse relation
term editor: Christopher J. Mungall

sends output to
type: ObjectProperty
sub property of: connected to
editor note: 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.
term editor: Christopher J. Mungall

relation between physical entity and a process or stage
type: ObjectProperty
domain: independent continuant
range: occurrent
term editor: Christopher J. Mungall
curator note: 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).
term editor: Christopher J. Mungall

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).
term editor: Christopher J. Mungall

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))
term editor: Christopher J. Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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)
term editor: Christopher J. Mungall
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).
term editor: Christopher J. Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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).
term editor: Christopher J. Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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
term editor: Christopher J. Mungall

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
term editor: Christopher J. Mungall
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).
term editor: Christopher J. Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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.
term editor: Christopher J. Mungall
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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
definition source: 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.
term editor: Christopher J. Mungall
definition source: causal-relations
curator note: 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
term editor: Christopher J. Mungall

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
editor note: 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.
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
sub property of: has participant
example of usage: '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
term editor: Christopher J. Mungall
alternative label: has intermediate product
in_subset: eco subset

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
editor note: 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
term editor: Christopher J. Mungall
definition source: causal-relations
curator note: 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
example of usage: 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.
editor note: 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
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/24330602
OBO foundry unique label: determined by (system to material entity)
creator: Pier Luigi Buttigieg
creator: Christopher J. Mungall
in_subset: eco subset

determines
type: ObjectProperty
sub property of: causally influences
definition: inverse of determined by
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

transcribed to
type: ObjectProperty
sub property of: genomically related to
definition: inverse of transcribed from
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
definition source: 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.
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
curator note: 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
example of usage: Every UTR is adjacent to a CDS of the same transcript
example of usage: Two consecutive DNA residues are sequentially adjacent
example of usage: 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
term editor: Christopher J. Mungall
definition source: 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
example of usage: 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
term editor: Christopher J. Mungall
alternative label: started by
definition source: 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
term editor: Christopher J. Mungall
alternative label: starts
definition source: 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
example of usage: 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
term editor: Christopher J. Mungall
alternative label: ended by
definition source: 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
term editor: Christopher J. Mungall
alternative label: ends
definition source: 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.
editor note: In the SO paper, this was defined as an instance-type relation
term editor: Christopher J. Mungall
definition source: 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
example of usage: 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
term editor: Christopher J. Mungall
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
example of usage: 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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
alternative label: contains
definition source: 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
term editor: Christopher J. Mungall
alternative label: 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.
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
alternative label: 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
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
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
example of usage: 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
term editor: Christopher J. Mungall
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
example of usage: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
definition: inverse of immediately downstream of
term editor: Christopher J. Mungall
cites as authority: 006650.abstract

has skeleton
type: ObjectProperty
sub property of: has part
inverse of: skeleton of
type: AsymmetricProperty
type: IrreflexiveProperty
domain: anatomical structure
range: material anatomical entity
example of usage: 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.
term editor: Christopher J. Mungall
alternative label: has supporting framework
curator note: 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
editor note: 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.
term editor: Christopher J. Mungall

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
editor note: 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
term editor: Christopher J. Mungall
definition source: http://eol.org/schema/terms/hyperparasitoidOf
definition source: 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
term editor: Christopher J. Mungall
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
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
in_subset: eco subset

has pathogen
type: ObjectProperty
sub property of: host of
term editor: Christopher J. Mungall
in_subset: eco subset

has evidence
type: ObjectProperty
sub property of: related via evidence or inference to
definition: inverse of is evidence for
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
definition source: 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)
term editor: Christopher J. Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
term editor: Christopher J. Mungall

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
term editor: Christopher J. Mungall
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).
term editor: Christopher J. Mungall
term editor: https://orcid.org/0000-0003-4639-4431
definition source: causal-relations
OBO foundry unique label: causally influences (entity-centric)

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
domain: anatomical structure
range: anatomical structure
definition: A relation that holds between elements of a musculoskeletal system or its analogs.
term editor: Christopher J. Mungall
curator note: 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.
term editor: Christopher J. Mungall
definition source: 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
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
definition source: UBERON:cjm
curator note: 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.
term editor: Christopher J. Mungall
definition source: Christopher J. Mungall
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
term editor: Christopher J. Mungall
in_subset: eco subset

has modifier
type: ObjectProperty
domain: characteristic
range: characteristic
definition: A relation that holds between an attribute or a qualifier and another attribute.
term editor: Christopher J. Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
curator note: 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
range: organism
term editor: Christopher J. Mungall
in_subset: eco subset

skeleton of
type: ObjectProperty
sub property of: part of
domain: anatomical structure
range: anatomical structure
definition: inverse of has skeleton
term editor: Christopher J. Mungall
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.
term editor: Christopher J. Mungall
definition source: 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
example of usage: 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
term editor: Christopher J. Mungall

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
editor note: 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 anatomical entity

results in assembly of
type: ObjectProperty
sub property of: results in formation of anatomical entity
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.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: Christopher J. Mungall
definition source: causal-relations

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

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: 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.
definition source: causal-relations

capable of inhibiting or preventing pathological process
type: ObjectProperty
sub property of: capable of negatively regulating
example of usage: 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.
alternative label: treats
definition source: causal-relations
curator note: 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: alternative label
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
example of usage: 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.
alternative label: causes disease
definition source: 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.
alternative label: treats
definition source: 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.
editor note: May be ceded to OBI

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: 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.
curator note: 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.
curator note: Groups both positive and negative correlation

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
example of usage: 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
curator note: 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
definition source: 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.
definition source: 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.
definition source: 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
definition source: 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
definition source: Types
definition source: 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.
definition source: 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.
definition source: 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.
definition source: Communal roosting

reservoir host of
type: ObjectProperty
sub property of: host of
inverse of: has reservoir host
example of usage: An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s.
definition: A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host.
definition source: v13071356
contributor: https://orcid.org/0000-0002-3120-4802
contributor: Jorrit Poelen
comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts.

has reservoir host
type: ObjectProperty
sub property of: has host
example of usage: An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s.
definition: inverse of reservoir host of
in_subset: defined by inverse

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
has curation status: 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.
term editor: 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
has curation status: pending final vetting
definition: a produced_by b iff some process that occurs_in b has_output a.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: https://orcid.org/0000-0002-1048-5019
alternative label: 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
example of usage: 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.
editor note: 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.
alternative label: 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.
alternative label: 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.
alternative label: 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
range: Class
  union of: process
  union of: quality
  union of: material entity
curator note: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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
curator note: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
creation date: 2017-11-05T03:20:01Z

is basis for realizable
type: ObjectProperty
sub property of: causally related to
created by: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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
curator note: 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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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.
editor note: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
curator note: 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: Christopher J. Mungall
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: Christopher J. Mungall
creation date: 2017-12-26T19:37:31Z

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable
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: Christopher J. Mungall
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: Christopher J. Mungall
creation date: 2017-12-26T19:50:53Z

disease arises from alteration in structure
type: ObjectProperty
sub property of: disease has basis in
range: 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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Christopher J. Mungall
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: Lynn Schriml

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: Lynn Schriml

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.
definition source: 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
definition source: 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
range: organism
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
range: organism
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 roost
type: ObjectProperty
sub property of: has habitat
domain: organism
range: habitat
example of usage: Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)
definition: x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.
contributor: Anne Thessen
date: 2023-01-18T14:28:21Z
in_subset: eco subset
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.

has substance added
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
example of usage: muffin 'has substance added' some 'baking soda'
has curation status: 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.
editor note: 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.
term editor: https://orcid.org/0000-0002-8844-9165

has substance removed
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
example of usage: 'egg white' 'has substance removed' some 'egg yolk'
has curation status: 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.
term editor: https://orcid.org/0000-0002-8844-9165

immersed in
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
example of usage: sardines 'immersed in' some 'oil and mustard'
has curation status: 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.
term editor: https://orcid.org/0000-0002-8844-9165

has consumer
type: ObjectProperty
domain: material entity
range: organism
example of usage: sardine has consumer some homo sapiens
has curation status: 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.
term editor: https://orcid.org/0000-0002-8844-9165

has primary substance added
type: ObjectProperty
sub property of: has substance added
type: IrreflexiveProperty
example of usage: bread 'has primary substance added' some 'flour'
has curation status: 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.
term editor: https://orcid.org/0000-0002-8844-9165

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable
range: process
property chain axiom: realized in
property chain axiom: causally downstream of
example of usage: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
example of usage: 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)
example of usage: 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: Austin Meier
contributor: Christopher J. Mungall
contributor: David Osumi-Sutherland
contributor: Marie-Angélique Laporte
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: Christopher J. Mungall

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
example of usage: Genetic information generically depend on molecules of DNA.
example of usage: The novel *War and Peace* generically depends on this copy of the novel.
example of usage: The pattern shared by chess boards generically depends on any chess board.
example of usage: The score of a symphony g-depends on a copy of the score.
example of usage: 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*.
definition source: [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
example of usage: Molecules of DNA are carriers of genetic information.
example of usage: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
example of usage: 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*
definition source: [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.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: indirectly activates

destabilizes quantity of
type: ObjectProperty
sub property of: directly negatively regulates quantity of
domain: material entity
range: material entity
example of usage: 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.
term editor: 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
example of usage: 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.
term editor: 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.
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: 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.
term editor: 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.
term editor: 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.
term editor: 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.
term editor: 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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
creation date: 2020-08-27T08:13:59Z

results in fusion of
type: ObjectProperty
sub property of: results in organization of
created by: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
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: Pascale Gaudet
creation date: 2022-09-26T06:08:01Z

positively regulates in another organism
type: ObjectProperty
sub property of: regulates in another organism
definition: x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase 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).
is positive form of: regulates in another organism
contributor: Pascale Gaudet
creation date: 2023-10-12T10:02:28Z
has_exact_synonym: positively regulates in other organism
in_subset: valid_for_go_ontology

negatively regulates in another organism
type: ObjectProperty
sub property of: regulates in another organism
definition: x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce 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).
is negative form of: regulates in another organism
contributor: Pascale Gaudet
creation date: 2023-10-12T10:02:42Z
has_exact_synonym: negatively regulates in other organism
in_subset: valid_for_go_ontology

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: https://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: https://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: https://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: https://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: https://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: https://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: https://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: https://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: https://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: https://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
example of usage: 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.
editor note: 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.
term editor: https://orcid.org/0000-0002-5260-9315
curator note: This relation is not meant to capture the relation between occurrents and data.

exemplar data of
type: ObjectProperty
sub property of: topObjectProperty
term editor: 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.
editor note: X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
term editor: Shawn Zheng Kai Tan
curator note: 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
example of usage: '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').
example of usage: 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.
editor note: 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.
curator note: 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: Shawn Zheng Kai Tan
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: Christopher J. Mungall

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: Christopher J. Mungall

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: Christopher J. Mungall

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: Christopher J. Mungall

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: Christopher J. Mungall

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: Christopher J. Mungall

has high plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: cell
example of usage: '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: Lindsay G Cowell
contributor: Anna Maria Masci

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
example of usage: '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: Lindsay G Cowell
contributor: Anna Maria Masci

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
curator note: Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.
contributor: Lauren E. Chan
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: Lauren E. Chan
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.
definition source: ExO:0000083
creator: Lauren E. Chan
date: 2021-12-14T20:41:45Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
example of usage: 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.
term editor: https://orcid.org/0000-0001-9625-1899
term editor: https://orcid.org/0000-0003-2620-0345
curator note: 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.
curator note: See github ticket https://github.com/oborel/obo-relations/issues/497
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

positively correlated with
type: ObjectProperty
sub property of: correlated with
type: SymmetricProperty
definition: A relation between entities in which one increases or decreases as the other does the same.
alternative label: directly correlated with
contributor: S. Clint Dowland

negatively correlated with
type: ObjectProperty
sub property of: correlated with
type: SymmetricProperty
type: IrreflexiveProperty
definition: A relation between entities in which one increases as the other decreases.
alternative label: inversely correlated with
contributor: S. Clint Dowland

contains measured amount
type: ObjectProperty
domain: container
range: measurement datum
example of usage: anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.
definition: A relation between a container and measurement datum that specifies the actual amount of material in the container.
contributor: Jie Zheng
contributor: Christian J Stoeckert

is myristoyltransferase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
definition: Helper relation for OWL definition of RO:0018002 myristoylates
contributor: Charles Tapley Hoyt

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: Charles Tapley Hoyt

myristoylated by
type: ObjectProperty
definition: inverse of myristoylates
contributor: Charles Tapley Hoyt

is agonist of
type: ObjectProperty
sub property of: directly positively regulates activity of
example of usage: 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: Charles Tapley Hoyt

is inverse agonist of
type: ObjectProperty
sub property of: directly negatively regulates activity of
example of usage: 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: Charles Tapley Hoyt

is antagonist of
type: ObjectProperty
sub property of: directly negatively regulates activity of
example of usage: 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: Charles Tapley Hoyt

chemical relationship
type: ObjectProperty
curator note: 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 chemical.
creator: Charles Tapley Hoyt

is direct conjugate base of
type: ObjectProperty
sub property of: is deprotonated form of
inverse of: is direct conjugate acid of
example of usage: pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)
definition: A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B.
is direct form of: is deprotonated form of
creator: Charles Tapley Hoyt

is direct conjugate acid of
type: ObjectProperty
sub property of: is protonated form of
example of usage: neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)
definition: A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B.
is direct form of: is protonated form of
creator: Charles Tapley Hoyt

is deprotonated form of
type: ObjectProperty
sub property of: chemical relationship
inverse of: is protonated form of
type: TransitiveProperty
example of usage: (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons.
definition: A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
creator: Charles Tapley Hoyt
database_cross_reference: obo:chebi#is_conjugate_base_of

is protonated form of
type: ObjectProperty
sub property of: chemical relationship
type: TransitiveProperty
example of usage: (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons.
definition: A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
creator: Charles Tapley Hoyt
database_cross_reference: obo:chebi#is_conjugate_acid_of

is matched small molecular pair with
type: ObjectProperty
sub property of: chemical relationship
type: SymmetricProperty
example of usage: phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol.
definition: A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
creator: Charles Tapley Hoyt
date: 2023-02-28T18:53:32Z
has_exact_synonym: is MMP with
has_exact_synonym: is matched molecular pair with

Axiom
annotated source: is matched small molecular pair with
annotated property: definition
annotated target: A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
source: ddr.21045
source: jm200452d
source: Matched molecular pair analysis

is tautomer of
type: ObjectProperty
sub property of: chemical relationship
type: SymmetricProperty
example of usage: 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
definition: Two chemicals are tautomers if they can be readily interconverted. This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
creator: Charles Tapley Hoyt
date: 2023-03-18T23:49:31Z
database_cross_reference: obo:chebi#is_tautomer_of
has_exact_synonym: is desmotrope of

Axiom
annotated source: is tautomer of
annotated property: example of usage
annotated target: 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.

is substitutent group from
type: ObjectProperty
sub property of: chemical relationship
example of usage: carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
definition: Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.
creator: Charles Tapley Hoyt
date: 2023-03-18T23:49:31Z
database_cross_reference: obo:chebi#is_substituent_group_from

Axiom
annotated source: is substitutent group from
annotated property: example of usage
annotated target: carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)

has functional parent
type: ObjectProperty
sub property of: chemical relationship
example of usage: hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
definition: Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
creator: Charles Tapley Hoyt
date: 2023-03-18T23:49:31Z
database_cross_reference: obo:chebi#has_functional_parent

Axiom
annotated source: has functional parent
annotated property: example of usage
annotated target: hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)

is enantiomer of
type: ObjectProperty
sub property of: chemical relationship
type: SymmetricProperty
example of usage: dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
definition: Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
creator: Charles Tapley Hoyt
date: 2023-03-18T23:49:31Z
database_cross_reference: obo:chebi#is_enantiomer_of
has_exact_synonym: is optical isomer of

Axiom
annotated source: is enantiomer of
annotated property: example of usage
annotated target: dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
comment: CHEBI_48557

has parent hydride
type: ObjectProperty
sub property of: chemical relationship
example of usage: pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
definition: Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.
creator: Charles Tapley Hoyt
date: 2023-03-18T23:49:31Z
database_cross_reference: obo:chebi#has_parent_hydride

Axiom
annotated source: has parent hydride
annotated property: example of usage
annotated target: pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.

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: James P. Balhoff

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: James P. Balhoff

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: James P. Balhoff

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: https://orcid.org/0000-0002-4142-7153

vessel supplies blood to
type: ObjectProperty
sub property of: supplies
domain: blood vessel
range: anatomical structure
example of usage: brachial artery vessel supplies blood to brachialis muscle
definition: x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.
contributor: Aleix Puig-Barbé
date: 2024-02-01T10:09:22Z

vessel drains blood from
type: ObjectProperty
sub property of: drains
domain: blood vessel
range: anatomical structure
example of usage: cystic vein vessel drains blood from gallbladder
definition: x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.
contributor: Aleix Puig-Barbé
date: 2024-02-01T10:09:41Z

directly supplies and drains
type: ObjectProperty
sub property of: supplies
sub property of: drains
domain: capillary
range: anatomical structure
example of usage: alveolar capillary directly supplies and drains some alveolus
definition: x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.
contributor: Aleix Puig-Barbé
date: 2024-02-01T10:09:59Z

disease relationship
type: ObjectProperty
definition: This relation groups relations between diseases and any other kind of entity.
curator note: 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: Christopher J. Mungall
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: Christopher J. Mungall
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.
editor note: 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: David Osumi-Sutherland
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: characteristic
disjoint with: generically dependent continuant
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
comment: 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: part of
  all values from: process
subclass of: Restriction
  on property: has prototype
  all values from: process
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
comment: 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
disjoint with: role

realizable
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: realizable
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.
label: realizable entity

quality
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: quality

characteristic
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: characteristic
subclass of: Restriction
  on property: has part
  all values from: characteristic
disjoint with: generically dependent continuant
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
comment: 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.
label: specifically dependent continuant

role
type: Class
subclass of: realizable
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: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
comment: 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

cell
type: Class
subclass of: anatomical structure
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.
definition: A material entity that has a plasma membrane and results from cellular division.
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: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
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).
comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.

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: 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

measurement datum
type: Class

exposure of organism
type: Class
subclass of: process
definition: A process during which an organism comes into contact with another entity.

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

habitat
type: Class
subclass of: environmental system
definition: An environmental system which can sustain and allow the growth of an ecological population.
database_cross_reference: EcoLexicon:habitat
database_cross_reference: LTER:238
database_cross_reference: SWEETRealm:Habitat
database_cross_reference: https://en.wikipedia.org/wiki/Habitat
comment: A habitat's specificity to an ecological population differentiates it from other environment classes.

Axiom
annotated source: habitat
annotated property: definition
annotated target: An environmental system which can sustain and allow the growth of an ecological population.
database_cross_reference: EnvO:EnvO

molecular_function
type: Class
subclass of: process
disjoint with: biological_process
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.
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.
comment: This is the same as GO molecular function
label: gene product or complex activity

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.
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.
has_broad_synonym: E2
has_broad_synonym: E3
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

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

The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-68712

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 MAVS
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

TRAF2,6 ubiquitinates NLRC5
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9750946

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

Ubiquitination of IKBKG by TRAF6
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9758604

ITCH polyubiquitinates MLKL at K50
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9793444

PRKN polyubiquitinates RIPK3
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9793485

LUBAC ubiquitinates RIPK1 at K627
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9793679

MIB2 ubiquitinates RIPK1 at K377, K604, K634
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9796346

STUB1 ubiquitinates RIPK1 at K571, K604, K627
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9796387

MIB2 ubiquitinates CFLAR
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9796626

MIB2 ubiquitinates CYLD at K338, K530
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9815507

SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex
type: Axiom
annotated source: ubiquitin-protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9817362

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

nucleus
type: Class
subclass of: material entity
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
label: cell nucleus

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
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: molecular_function
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.
definition: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
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: A biological process is an evolved process
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.
label: biological process

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred term: information content entity

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
editor preferred term: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

processed material
type: Class
subclass of: material entity
editor preferred term: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

container
type: Class
subclass of: device
editor preferred term: container
has curation status: metadata incomplete
definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
term editor: PERSON: Bjoern Peters

device
type: Class
subclass of: processed material
editor preferred term: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI development call 2012-12-17.

organism
type: Class
subclass of: material entity
editor preferred term: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: ready for release
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

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: characteristic
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

obsolete exposure event or process
type: Class
example of usage: 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,
example of usage: 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: OBSOLETE 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.
editor note: 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: Christopher J. Mungall
created by: Christopher J. Mungall
creation date: 2017-06-05T17:55:39Z
deprecated: true

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.
term editor: Christopher J. Mungall

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
term editor: Christopher J. Mungall
curator note: 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
term editor: Christopher J. Mungall
curator note: 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.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
term editor: Christopher J. Mungall
definition source: http://www.jbiomedsem.com/content/4/1/43

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.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: SCTID:362889002
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
database_cross_reference: http://dbpedia.org/ontology/AnatomicalStructure
has_exact_synonym: biological structure
has_exact_synonym: connected biological structure
id: UBERON:0000061
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: has_exact_synonym
annotated target: connected biological structure
database_cross_reference: CARO:0000003

neuron projection bundle
type: Class
subclass of: anatomical structure
definition: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
database_cross_reference: CARO:0001001
database_cross_reference: NLX:147821
has_exact_synonym: funiculus
has_exact_synonym: nerve fiber bundle
has_exact_synonym: neural fiber bundle
id: UBERON:0000122

Axiom
annotated source: neuron projection bundle
annotated property: definition
annotated target: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
database_cross_reference: CARO:0001001
database_cross_reference: FBC:DOS
database_cross_reference: FBbt:00005099

Axiom
annotated source: neuron projection bundle
annotated property: has_exact_synonym
annotated target: nerve fiber bundle
database_cross_reference: FBbt:00005099

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
disjoint with: immaterial anatomical entity
definition: Anatomical entity that has mass.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
id: UBERON:0000465
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: Anatomical entity that has mass.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

immaterial anatomical entity
type: Class
subclass of: immaterial entity
subclass of: anatomical entity
definition: Anatomical entity that has no mass.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010265
database_cross_reference: AEO:0000007
database_cross_reference: BILA:0000007
database_cross_reference: CARO:0000007
database_cross_reference: EHDAA2:0003007
database_cross_reference: FMA:67112
database_cross_reference: HAO:0000007
database_cross_reference: TAO:0001835
database_cross_reference: TGMA:0001827
database_cross_reference: VHOG:0001727
has_exact_synonym: immaterial physical anatomical entity
id: UBERON:0000466
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: immaterial anatomical entity
annotated property: definition
annotated target: Anatomical entity that has no mass.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: immaterial anatomical entity
annotated property: has_exact_synonym
annotated target: immaterial physical anatomical entity
database_cross_reference: FMA:67112

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BFO:0000004
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
id: UBERON:0001062
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
database_cross_reference: FMA:62955
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: database_cross_reference
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

blood vessel
type: Class
subclass of: multicellular anatomical structure
definition: A vessel through which blood circulates in the body.
editor note: consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
has_broad_synonym: vascular element
database_cross_reference: AAO:0011004
database_cross_reference: AEO:0000207
database_cross_reference: BTO:0001102
database_cross_reference: CALOHA:TS-0080
database_cross_reference: EFO:0000817
database_cross_reference: EHDAA2:0003252
database_cross_reference: EHDAA:240
database_cross_reference: EMAPA:32743
database_cross_reference: EMAPA:35993
database_cross_reference: FMA:50722
database_cross_reference: FMA:63183
database_cross_reference: GAID:169
database_cross_reference: MA:0000060
database_cross_reference: MAT:0000393
database_cross_reference: MESH:D001808
database_cross_reference: NCIT:C12679
database_cross_reference: NLXANAT:090901
database_cross_reference: SCTID:361097006
database_cross_reference: TAO:0002137
database_cross_reference: UMLS:C0005847
database_cross_reference: VHOG:0001250
database_cross_reference: Wikipedia:Blood_vessel
database_cross_reference: XAO:0001011
database_cross_reference: ZFA:0005314
has_exact_synonym: region of vascular tree organ
has_exact_synonym: vascular tree organ region
id: UBERON:0001981
in_subset: efo slim
in_subset: human reference atlas
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: blood vessel
annotated property: definition
annotated target: A vessel through which blood circulates in the body.
database_cross_reference: BTO:0001102
database_cross_reference: Wikipedia:Blood_vessel

Axiom
annotated source: blood vessel
annotated property: has_broad_synonym
annotated target: vascular element
database_cross_reference: EMAPA:35993

Axiom
annotated source: blood vessel
annotated property: database_cross_reference
annotated target: UMLS:C0005847
source: ncithesaurus:Blood_Vessel

Axiom
annotated source: blood vessel
annotated property: has_exact_synonym
annotated target: region of vascular tree organ
database_cross_reference: FMA:50722

Axiom
annotated source: blood vessel
annotated property: has_exact_synonym
annotated target: vascular tree organ region
database_cross_reference: FMA:50722

capillary
type: Class
subclass of: blood vessel
definition: Any of the smallest blood vessels connecting arterioles with venules.
editor note: not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
database_cross_reference: AAO:0010252
database_cross_reference: BTO:0002045
database_cross_reference: CALOHA:TS-2006
database_cross_reference: EFO:0001906
database_cross_reference: EMAPA:35198
database_cross_reference: EV:0100035
database_cross_reference: FMA:63194
database_cross_reference: MA:0000065
database_cross_reference: MESH:D002196
database_cross_reference: NCIT:C12685
database_cross_reference: NLXANAT:090902
database_cross_reference: TAO:0005250
database_cross_reference: UMLS:C0935624
database_cross_reference: VHOG:0001253
database_cross_reference: Wikipedia:Capillary
database_cross_reference: XAO:0000116
database_cross_reference: ZFA:0005250
has_exact_synonym: blood capillary
has_exact_synonym: capillary vessel
id: UBERON:0001982
in_subset: efo slim
in_subset: human reference atlas
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: capillary
annotated property: definition
annotated target: Any of the smallest blood vessels connecting arterioles with venules.
database_cross_reference: ISBN:0073040584
database_cross_reference: Wikipedia:Capillary
database_cross_reference: https://github.com/obophenotype/uberon/issues/137

Axiom
annotated source: capillary
annotated property: database_cross_reference
annotated target: UMLS:C0935624
source: ncithesaurus:Capillary

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: CARO:0010000
has_exact_synonym: multicellular structure
id: UBERON:0010000
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: multicellular anatomical structure
annotated property: definition
annotated target: An anatomical structure that has more than one cell as a part.
database_cross_reference: CARO:0010000

Axiom
annotated source: multicellular anatomical structure
annotated property: has_exact_synonym
annotated target: multicellular structure
database_cross_reference: FBbt:00100313

phenotype
type: Class
subclass of: quality

example to be eventually removed
type: NamedIndividual
editor preferred term: example to be eventually removed

metadata complete
type: NamedIndividual
editor preferred term: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
editor preferred term: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
editor preferred term: ready for release
has curation status: pending final vetting
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
editor preferred term: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
editor preferred term: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred term: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

to be replaced with external ontology term
type: NamedIndividual
editor preferred term: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred term: requires discussion
has curation status: pending final vetting
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI

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)

Aleix Puig-Barbé
type: NamedIndividual
description: Researcher ORCID=0000-0001-6677-8489

Axiom
annotated source: Aleix Puig-Barbé
annotated property: description
annotated target: Researcher ORCID=0000-0001-6677-8489
source: Q123250332

Axiom
annotated source: Aleix Puig-Barbé
annotated property: label
annotated target: Aleix Puig-Barbé
source: Q123250332

Austin Meier
type: NamedIndividual
description: Researcher

Axiom
annotated source: Austin Meier
annotated property: description
annotated target: Researcher
source: Q116041404

Axiom
annotated source: Austin Meier
annotated property: label
annotated target: Austin Meier
source: Q116041404

Shawn Zheng Kai Tan
type: NamedIndividual
description: researcher

Axiom
annotated source: Shawn Zheng Kai Tan
annotated property: description
annotated target: researcher
source: Q57023310

Axiom
annotated source: Shawn Zheng Kai Tan
annotated property: label
annotated target: Shawn Zheng Kai Tan
source: Q57023310

Lynn Schriml
type: NamedIndividual
description: researcher, metadata, diseases, University of Maryland

Axiom
annotated source: Lynn Schriml
annotated property: description
annotated target: researcher, metadata, diseases, University of Maryland
source: Q28913673

Axiom
annotated source: Lynn Schriml
annotated property: label
annotated target: Lynn Schriml
source: Q28913673

Anne Thessen
type: NamedIndividual
description: data scientist

Axiom
annotated source: Anne Thessen
annotated property: description
annotated target: data scientist
source: Q47503085

Axiom
annotated source: Anne Thessen
annotated property: label
annotated target: Anne Thessen
source: Q47503085

Jie Zheng
type: NamedIndividual
description: researcher (ORCID 0000-0002-2999-0103)

Axiom
annotated source: Jie Zheng
annotated property: description
annotated target: researcher (ORCID 0000-0002-2999-0103)
source: Q90780528

Axiom
annotated source: Jie Zheng
annotated property: label
annotated target: Jie Zheng
source: Q90780528

Pier Luigi Buttigieg
type: NamedIndividual
description: researcher

Axiom
annotated source: Pier Luigi Buttigieg
annotated property: description
annotated target: researcher
source: Q41566750

Axiom
annotated source: Pier Luigi Buttigieg
annotated property: label
annotated target: Pier Luigi Buttigieg
source: Q41566750

Christian J Stoeckert
type: NamedIndividual
description: researcher

Axiom
annotated source: Christian J Stoeckert
annotated property: description
annotated target: researcher
source: Q67220657

Axiom
annotated source: Christian J Stoeckert
annotated property: label
annotated target: Christian J Stoeckert
source: Q67220657

Christopher J. Mungall
type: NamedIndividual
description: bioinformatics researcher

Axiom
annotated source: Christopher J. Mungall
annotated property: description
annotated target: bioinformatics researcher
source: Q20746118

Axiom
annotated source: Christopher J. Mungall
annotated property: label
annotated target: Christopher J. Mungall
source: Q20746118

David Osumi-Sutherland
type: NamedIndividual
description: researcher

Axiom
annotated source: David Osumi-Sutherland
annotated property: description
annotated target: researcher
source: Q54303418

Axiom
annotated source: David Osumi-Sutherland
annotated property: label
annotated target: David Osumi-Sutherland
source: Q54303418

Lauren E. Chan
type: NamedIndividual
description: researcher

Axiom
annotated source: Lauren E. Chan
annotated property: description
annotated target: researcher
source: Q108416491

Axiom
annotated source: Lauren E. Chan
annotated property: label
annotated target: Lauren E. Chan
source: Q108416491

Marie-Angélique Laporte
type: NamedIndividual
description: researcher

Axiom
annotated source: Marie-Angélique Laporte
annotated property: description
annotated target: researcher
source: Q63389961

Axiom
annotated source: Marie-Angélique Laporte
annotated property: label
annotated target: Marie-Angélique Laporte
source: Q63389961

James P. Balhoff
type: NamedIndividual
description: researcher

Axiom
annotated source: James P. Balhoff
annotated property: description
annotated target: researcher
source: Q37649212

Axiom
annotated source: James P. Balhoff
annotated property: label
annotated target: James P. Balhoff
source: Q37649212

Lindsay G Cowell
type: NamedIndividual
description: researcher

Axiom
annotated source: Lindsay G Cowell
annotated property: description
annotated target: researcher
source: Q89259560

Axiom
annotated source: Lindsay G Cowell
annotated property: label
annotated target: Lindsay G Cowell
source: Q89259560

Pascale Gaudet
type: NamedIndividual
description: Canadian biocurator

Axiom
annotated source: Pascale Gaudet
annotated property: description
annotated target: Canadian biocurator
source: Q30032484

Axiom
annotated source: Pascale Gaudet
annotated property: label
annotated target: Pascale Gaudet
source: Q30032484

S. Clint Dowland
type: NamedIndividual
description: Researcher ORCID=0000-0003-1909-9269

Axiom
annotated source: S. Clint Dowland
annotated property: description
annotated target: Researcher ORCID=0000-0003-1909-9269
source: Q123250399

Axiom
annotated source: S. Clint Dowland
annotated property: label
annotated target: S. Clint Dowland
source: Q123250399

Anna Maria Masci
type: NamedIndividual
description: researcher

Axiom
annotated source: Anna Maria Masci
annotated property: description
annotated target: researcher
source: Q37377046

Axiom
annotated source: Anna Maria Masci
annotated property: label
annotated target: Anna Maria Masci
source: Q37377046

Jorrit Poelen
type: NamedIndividual
description: software/data engineer

Axiom
annotated source: Jorrit Poelen
annotated property: description
annotated target: software/data engineer
source: Q58206618

Axiom
annotated source: Jorrit Poelen
annotated property: label
annotated target: Jorrit Poelen
source: Q58206618

Charles Tapley Hoyt
type: NamedIndividual
description: American chemist

Axiom
annotated source: Charles Tapley Hoyt
annotated property: description
annotated target: American chemist
source: Q47475003

Axiom
annotated source: Charles Tapley Hoyt
annotated property: label
annotated target: Charles Tapley Hoyt
source: Q47475003

data item
editor preferred term: data item

data about an ontology part
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

failed exploratory term
editor preferred term: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

in branch
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

obsolete_core
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

obsolescence reason specification
editor preferred term: obsolescence reason specification
has curation status: pending final vetting
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

placeholder removed
editor preferred term: placeholder removed

terms merged
editor preferred term: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
editor preferred term: term imported
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
editor preferred term: term split
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

has obsolescence reason
editor preferred term: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

ontology term requester
editor preferred term: ontology term requester
has curation status: pending final vetting
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

denotator type
editor preferred term: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

universal
editor preferred term: universal
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

is denotator type
editor preferred term: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

defined class
editor preferred term: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
term editor: Alan Ruttenberg

named class expression
editor preferred term: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
term editor: Alan Ruttenberg

antisymmetric property
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg

has ID digit count
editor preferred term: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
editor preferred term: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
editor preferred term: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
editor preferred term: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

has associated axiom(nl)
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
editor preferred term: is allocated id range
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

may be identical to
editor preferred term: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
editor preferred term: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng

has axiom label
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

ontology module
editor preferred term: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative label: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.

base ontology module
editor preferred term: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
editor preferred term: editors ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative label: source ontology module

main release ontology module
editor preferred term: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
editor preferred term: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
editor preferred term: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

subset ontology module
editor preferred term: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

curation subset ontology module
editor preferred term: curation subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

analysis subset ontology module
editor preferred term: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
editor preferred term: single layer ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative label: ribbon subset

exclusion subset ontology module
editor preferred term: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

external import ontology module
editor preferred term: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

species subset ontology module
editor preferred term: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

reasoned ontology module
editor preferred term: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
editor preferred term: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
editor preferred term: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
editor preferred term: taxonomic bridge ontology module

ontology module subsetted by expressivity
editor preferred term: ontology module subsetted by expressivity

obo basic subset ontology module
editor preferred term: obo basic subset ontology module
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

ontology module subsetted by OWL profile
editor preferred term: ontology module subsetted by OWL profile

EL++ ontology module
editor preferred term: EL++ ontology module

out of scope
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
term editor: http://orcid.org/0000-0001-5208-3432

logical characteristic of object property
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

abbreviation
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initalisms
contributor: Charles Tapley Hoyt

ambiguous synonym
definition: A synonym type for describing ambiguous synonyms
contributor: Charles Tapley Hoyt

dubious synonym
definition: A synonym type for describing dubious synonyms
contributor: Charles Tapley Hoyt

layperson synonym
example of usage: EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
definition: A synonym type for describing layperson or colloquial synonyms
contributor: Charles Tapley Hoyt

plural form
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
definition: A synonym type for describing pluralization synonyms
contributor: Charles Tapley Hoyt

UK spelling synonym
example of usage: CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
definition: A synonym type for describing UK spelling variants
contributor: Charles Tapley Hoyt

misspelling
definition: A synonym type for common misspellings
contributor: Charles Tapley Hoyt

misnomer
definition: A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
contributor: Charles Tapley Hoyt

previous name
example of usage: MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
definition: A synonym type for names that have been used as primary labels in the past.
contributor: Charles Tapley Hoyt

legal name
example of usage: The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
definition: A synonym type for the legal entity name
contributor: Charles Tapley Hoyt

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 effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
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 effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
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: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
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: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
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: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
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: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'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: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

Restriction
on property: is ubiquitination
has self: true