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

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.

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 . }

defined by inverse
type: AnnotationProperty

logical macro assertion on an annotation property
type: AnnotationProperty

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

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

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.

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).

is positive form of
type: AnnotationProperty
created by: Christopher J. Mungall
creation date: 2018-03-14T00:03:16Z

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

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.

valid_for_go_annotation_extension
type: AnnotationProperty
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-09-22T11:05:29Z

valid_for_go_gp2term
type: AnnotationProperty
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-09-22T11:05:18Z

valid_for_go_ontology
type: AnnotationProperty
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-09-22T11:04:12Z

valid_for_gocam
type: AnnotationProperty
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-09-22T11:05:45Z

eco subset
type: AnnotationProperty

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

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

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

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

in_subset
type: AnnotationProperty

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

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
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

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
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

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.

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

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 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

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

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
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.

immediately precedes
type: ObjectProperty
sub property of: precedes
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

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

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))))

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

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: 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.

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
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

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

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

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

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: 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
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
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

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

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.

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

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
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
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

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 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

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 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

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

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 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

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

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

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.

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

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

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 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

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

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

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

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

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 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

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

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
RO_0002579: positively regulates

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
RO_0002579: 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

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

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

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: Considering relabeling as 'pairwise interacts with'
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.
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

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

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
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

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 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

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

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
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 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 ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part 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.

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

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
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
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

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 part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between entities
domain: system
range: material entity
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

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

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

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

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 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

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

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 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

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

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

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.

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

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

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.

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

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

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

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: https://orcid.org/0000-0001-6996-0040
contributor: Christopher J. Mungall
contributor: David Osumi-Sutherland
contributor: https://orcid.org/0000-0002-8461-9745
has_exact_synonym: triggered by process

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

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: https://orcid.org/0000-0003-1813-6857
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: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:08:01Z

has synaptic IO in region
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
created by: 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.

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

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: https://orcid.org/0000-0002-7463-6306
date: 2021-11-05T17:30:14Z

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.
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
contributor: William D Duncan
contributor: Asiyah Yu Lin
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

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

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

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

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

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

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.
RO_0002175: NCBITaxon 9606
database_cross_reference: BTO:0000938
database_cross_reference: CALOHA:TS-0683
database_cross_reference: FBbt:00005106
database_cross_reference: FMA:54527
database_cross_reference: VHOG:0001483
database_cross_reference: WBbt:0003679
has_exact_synonym: nerve cell
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.

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

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

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

molecular_function
type: Class
subclass of: 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
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

planned process
type: Class
subclass of: process
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived

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

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.

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.
RO_0002175: NCBITaxon_33090
RO_0002175: 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
definition: Anatomical entity that has mass.
RO_0002175: NCBITaxon_33090
RO_0002175: 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

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.
RO_0002175: NCBITaxon_33090
RO_0002175: 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

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
RO_0002175: NCBITaxon_33090
RO_0002175: 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

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

William D Duncan
type: NamedIndividual
description: researcher

Axiom
annotated source: William D Duncan
annotated property: description
annotated target: researcher
source: Q89881908

Axiom
annotated source: William D Duncan
annotated property: label
annotated target: William D Duncan
source: Q89881908

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

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

Asiyah Yu Lin
type: NamedIndividual
description: Researcher ORCID=0000-0003-2620-0345

Axiom
annotated source: Asiyah Yu Lin
annotated property: description
annotated target: Researcher ORCID=0000-0003-2620-0345
source: Q123250403

Axiom
annotated source: Asiyah Yu Lin
annotated property: label
annotated target: Asiyah Yu Lin
source: Q123250403

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

Restriction
on property: is ubiquitination
has self: true