definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
IAO_0000111: editor note
IAO_0000114: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term tracker item
type: AnnotationProperty
IAO_0000111: term tracker item
IAO_0000112: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
IAO_0000114: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
IAO_0000117: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
IAO_0000119: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

term replaced by
type: AnnotationProperty
IAO_0000111: term replaced by
IAO_0000114: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

never in taxon
type: AnnotationProperty
IAO_0000112: tooth SubClassOf 'never in taxon' value 'Aves'
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
IAO_0000425: Class: ?X DisjointWith: RO_0002162 some ?Y
OMO_0002000: 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 . }

present in taxon
type: AnnotationProperty
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.

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.

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.
IAO_0000117: 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
IAO_0000112: disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/123
contributor: https://orcid.org/0000-0002-7356-1779
created: 2024-03-18
label: has cross-reference

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.
IAO_0000117: 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.
IAO_0000117: 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.
IAO_0000117: 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
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
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'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable entity
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: BFO_0000031
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
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'.
IAO_0000118: has_part
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
IAO_0000111: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
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.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: ro-eco

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

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

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

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
IAO_0000118: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
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.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
RO_0001900: RO_0001901

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

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
IAO_0000118: function_of
IAO_0000118: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

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

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
IAO_0000118: is role of
IAO_0000118: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
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.
IAO_0000118: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000112: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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.
IAO_0000118: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
IAO_0000118: has_role

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

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in_subset: RO_0002259
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.

bounding layer of
type: ObjectProperty
sub property of: part of
domain: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has characteristic
    some values from: laminar
range: material entity
definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: ro-eco
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
domain: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
editor note: Note from NCEAS meeting: consider changing primary label
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: ro-eco
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

regulates in another organism
type: ObjectProperty
sub property of: causally upstream of or within
domain: process
range: process
definition: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
IAO_0000117: https://orcid.org/0000-0002-7073-9172
has_exact_synonym: regulates in other organism
in_subset: valid for go ontology

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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has necessary component activity
type: ObjectProperty
sub property of: has component activity
sub property of: positively regulated by
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:36:08Z
comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.

has component activity
type: ObjectProperty
sub property of: has component process
created by: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-19T17:30:36Z

occurs across
type: ObjectProperty
sub property of: has part that occurs in
definition: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-20T17:19:37Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172

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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172

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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172

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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in_subset: ro-eco
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
property chain axiom: ends with
property chain axiom: starts with
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: io
in_subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: d
IAO_0000118: during
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: o
IAO_0000118: overlaps
in_subset: ro-eco
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
property chain axiom: is neuron
property chain axiom: is anatomical entity
IAO_0000114: pending final vetting
definition: Relation between a neuron and a material anatomical entity that its soma is part of.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
RO_0001900: RO_0001901

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco

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

only in taxon
type: ObjectProperty
sub property of: in taxon
IAO_0000112: lactation SubClassOf 'only in taxon' some 'Mammalia'
IAO_0000114: pending final vetting
definition: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
editor note: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: organism
property chain axiom: overlaps
property chain axiom: regulates
property chain axiom: capable of
property chain axiom: has developmental contribution from
property chain axiom: results in developmental progression of
property chain axiom: has potential to develop into
property chain axiom: produces
property chain axiom: produced by
IAO_0000114: pending final vetting
definition: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
IAO_0000117: 0000-0001-9227-417X
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
has_narrow_synonym: life cycle stage of
in_subset: ro-eco
comment: Connects a biological entity to its taxon of origin.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: ro-eco

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

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
IAO_0000114: pending final vetting
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
IAO_0000114: pending final vetting
definition: inverse of develops from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
in_subset: RO_0002259

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: ends with
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
IAO_0000117: https://orcid.org/0000-0001-7476-6306
IAO_0000117: https://orcid.org/0000-0002-3837-8864
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: 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
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in_subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function in

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

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Allen's interval algebra
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

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

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

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

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

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: starts with
property chain axiom: occurs in
IAO_0000114: pending final vetting
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts with process that occurs in
in_subset: ro-eco

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: ends with
property chain axiom: occurs in
IAO_0000114: pending final vetting
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends with process that occurs in
in_subset: ro-eco

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

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

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
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: pending final vetting
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
IAO_0000114: pending final vetting
definition: inverse of has developmental contribution from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
IAO_0000114: pending final vetting
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
editor note: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in_subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in_subset: valid for go gp2term

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

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: GO_0008150
range: anatomical entity
IAO_0000114: pending final vetting
definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in development of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000114: pending final vetting
definition: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in formation of anatomical entity
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
IAO_0000112: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
IAO_0000112: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
IAO_0000114: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in morphogenesis of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
IAO_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: pending final vetting
definition: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in maturation of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
IAO_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: pending final vetting
definition: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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.
RO_0004049: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO_0004050: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

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

results in acquisition of features of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
range: anatomical structure
IAO_0000112: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
definition: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in_subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: false

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

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

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: process
range: material entity
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
definition: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: regulates levels of (process to entity)

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

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

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

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in transport along
type: ObjectProperty
sub property of: related via localization to
definition: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in transport across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in
definition: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go ontology

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

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

results in commitment to
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
IAO_0000112: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
definition: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in determination of
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
definition: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259
in_subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259
in_subset: ro-eco

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

results in structural organization of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
definition: A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in specification of
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
definition: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
IAO_0000114: requires discussion
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

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

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: requires discussion
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.

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

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

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

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly activates
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: 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…
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

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

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

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of

provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: has output
property chain axiom: has input
definition: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly provides input for
IAO_0000119: causal-relations
IAO_0000589: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of or within, positive effect
type: TransitiveProperty
domain: process
range: process
IAO_0000114: requires discussion
definition: transitive form of directly_provides_input_for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
IAO_0000589: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
property chain axiom: part of
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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
in_subset: RO_0002259

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

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0004050: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: involved in or reguates

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

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

Axiom
annotated source: is active in
annotated property: definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: https://orcid.org/0000-0002-7073-9172

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
editor note: Considering relabeling as 'pairwise interacts with'
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has_exact_synonym: in pairwise interaction with
in_subset: ro-eco

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

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

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

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

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

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in_subset: ro-eco

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

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

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

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

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

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

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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)

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

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: 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
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

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

results in assembly of
type: ObjectProperty
sub property of: results in formation of anatomical entity
sub property of: results in organization of
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

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

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

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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations

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

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

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

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

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: 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
IAO_0000114: pending final vetting
definition: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in_subset: ro-eco
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.

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

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

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

Axiom
annotated source: has primary output
annotated property: definition
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

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

Axiom
annotated source: has primary input
annotated property: definition
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

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

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

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

has small molecule regulator
type: ObjectProperty
sub property of: has participant
inverse of: is small molecule regulator of
definition: a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-04-22T20:27:26Z

has small molecule activator
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule activator of
definition: a relation between a process and a continuant, in which the process is activated by the small molecule continuant
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-04-22T20:28:37Z

has small molecule inhibitor
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule inhibitor of
definition: a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-04-22T20:28:54Z

acts on population of
type: ObjectProperty
sub property of: has participant
definition: p acts on population of c iff c' is a collection, has members of type c, and p has participant c
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-08T17:21:33Z
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

is small molecule regulator of
type: ObjectProperty
sub property of: capable of regulating
definition: a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-24T13:15:17Z

is small molecule activator of
type: ObjectProperty
sub property of: capable of positively regulating
sub property of: is small molecule regulator of
definition: a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-24T13:15:26Z

is small molecule inhibitor of
type: ObjectProperty
sub property of: capable of negatively regulating
sub property of: is small molecule regulator of
definition: a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2020-06-24T13:15:35Z

results in fusion of
type: ObjectProperty
sub property of: results in organization of
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2021-02-26T07:28:29Z
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

positively regulates in another organism
type: ObjectProperty
sub property of: regulates in another organism
definition: x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
RO_0004049: regulates in another organism
contributor: https://orcid.org/0000-0003-1813-6857
creation date: 2023-10-12T10:02:28Z
has_exact_synonym: positively regulates in other organism
in_subset: valid for go ontology

negatively regulates in another organism
type: ObjectProperty
sub property of: regulates in another organism
definition: x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
RO_0004050: regulates in another organism
contributor: https://orcid.org/0000-0003-1813-6857
creation date: 2023-10-12T10:02:42Z
has_exact_synonym: negatively regulates in other organism
in_subset: valid for go ontology

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

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

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

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

is neuron
type: ObjectProperty
domain: neuron
definition: This property only applies to neurons
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-10-23T14:34:52Z

is anatomical entity
type: ObjectProperty
domain: anatomical entity
definition: This property only applies to anatomical entities.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-10-29T09:55:07Z

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

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

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

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
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.

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 entity
disjoint with: role

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

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

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

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

function
type: Class
subclass of: disposition

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

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

cell
type: Class
subclass of: anatomical structure
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
editor note: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
editor note: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: MESH:D002477
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

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

sensory neuron
type: Class
subclass of: neuron
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001037
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
equivalent class: Restriction
  on property: is neuron
  has self: true
subclass of: cell
definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000938
database_cross_reference: CALOHA:TS-0683
database_cross_reference: 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

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
IAO_0000111: curation status specification
IAO_0000114: 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)
IAO_0000117: PERSON:Bill Bug
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO_0000119: OBI_0000266

organism
type: Class
subclass of: material entity
IAO_0000111: organism
IAO_0000112: animal
IAO_0000112: fungus
IAO_0000112: plant
IAO_0000112: virus
IAO_0000114: 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.
IAO_0000117: GROUP: OBI Biomaterial Branch
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Organism

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
database_cross_reference: PATOC:GVG

linear
type: Class
subclass of: quality
definition: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
id: PATO:0001199

Axiom
annotated source: linear
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
database_cross_reference: ISBN:0881923214

laminar
type: Class
subclass of: quality
definition: A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
contributor: 0000-0002-2061-091X
creation date: 2009-10-06T04:37:14Z
id: PATO:0002124

Axiom
annotated source: laminar
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
database_cross_reference: PATOC:GVG

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: SCTID:362889002
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
database_cross_reference: http://dbpedia.org/ontology/AnatomicalStructure
has_exact_synonym: biological structure
has_exact_synonym: connected biological structure
id: UBERON:0000061
in_subset: common anatomy
in_subset: human reference atlas
in_subset: human subset
in_subset: mouse subset
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

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
definition: Anatomical entity that has mass.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
id: UBERON:0000465
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
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
equivalent class: Restriction
  on property: is anatomical entity
  has self: true
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon 4751
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BFO:0000004
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
id: UBERON:0001062
in_subset: common anatomy
in_subset: human subset
in_subset: mouse subset
in_subset: upper level

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

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

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

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

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

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

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

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

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

Western Australian Mulga Shrublands Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:25:21Z
has_broad_synonym: Western Australia Ecoregion
database_cross_reference: WWF:AA1310
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1310

Australasia Ecoregion
type: NamedIndividual
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:51:32Z
database_cross_reference: https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands

Tirari-Sturt Stony Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:52:41Z
has_broad_synonym: Southern central Australia Ecoregion
database_cross_reference: WWF:AA1309
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1309

Simpson Desert Region
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:54:35Z
has_broad_synonym: Eastern central Australia Ecoregion
database_cross_reference: WWF:AA1308
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1308

Pilbara Shrublands Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:56:13Z
has_broad_synonym: Western Australia Ecoregion
database_cross_reference: WWF:AA1307
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1307

Carnarvon Xeric Shrublands Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:10:52Z
has_broad_synonym: Western coast of Australia Ecoregion
database_cross_reference: WWF:AA1301
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1301

Central Ranges Xeric Shrub Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:12:28Z
has_broad_synonym: Central Australia Ecoregion
database_cross_reference: WWF:AA1302
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1302

Gibson Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:15:11Z
has_broad_synonym: Western central Australia
database_cross_reference: WWF:AA1303
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1303

The Great Sandy-Tanami Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:17:15Z
has_broad_synonym: Northwestern Australia
database_cross_reference: WWF:AA1304
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1304

Great Victoria Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:24:06Z
has_broad_synonym: Southern Australia Ecoregion
database_cross_reference: WWF:AA1305
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1305

Nullarbor Plains Xeric Shrubland Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:26:16Z
has_broad_synonym: Southern Australia Ecoregion
database_cross_reference: WWF:AA1306
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1306

Afrotropical Ecoregion
type: NamedIndividual
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:01:41Z
database_cross_reference: https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands

Succulent Karoo Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:02:37Z
has_broad_synonym: Southern Africa: Southern Namibia into South Africa
database_cross_reference: WWF:AT1322
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1322

Yemen and Saudi Arabia Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:07:38Z
database_cross_reference: WWF:AT1321
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1321
has_exact_synonym: Arabian Peninsula: Yemen and Saudi Arabia

Yemen, Saudi Arabia, and Oman Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:11:38Z
database_cross_reference: WWF:AT1320
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1320
has_exact_synonym: Arabian Peninsula: Yemen, Saudi Arabia, and Oman

Somali Montane Xeric Woodland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:13:00Z
database_cross_reference: WWF:AT1319
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1319
has_exact_synonym: Somali montane xeric woodlands ecoregion

Socotran Archipelago Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:15:07Z
has_broad_synonym: Islands east of the Horn of Africa and south of Yemen Ecoregion
database_cross_reference: WWF:AT1318
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1318

Red Sea Coastal Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:18:55Z
database_cross_reference: WWF:AT1317
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1317

Namibian Savanna Woodland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:20:56Z
database_cross_reference: WWF:AT1316
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1316

Namib Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:24:28Z
has_broad_synonym: Africa: Namibia Ecoregion
database_cross_reference: WWF:AT1315
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1315

Nama Karoo Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:26:15Z
database_cross_reference: WWF:AT1314
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1314

Masai Xeric Grasslands and Shrublands Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:28:43Z
database_cross_reference: WWF:AT1313
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1313

Madagascar Succulent Woodlands Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:30:23Z
database_cross_reference: WWF:AT1312
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1312

Madagascar Spiny Thickets Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:31:29Z
database_cross_reference: WWF:AT1311
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1311
has_exact_synonym: Madagascar spiny desert ecoregion

Kaokoveld Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:39:32Z
database_cross_reference: WWF:AT1310
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1310
has_exact_synonym: Africa: Coastal Namibia and Angola Ecoregion

Kalahari Xeric Savanna Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:42:47Z
database_cross_reference: WWF:AT1309
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1309

Ile Europa and Bassas da India Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:44:54Z
database_cross_reference: WWF:AT1308
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1308
has_exact_synonym: Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion

Hobyo Grassland and Shrubland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:46:58Z
has_broad_synonym: Eastern Africa: Somalia
database_cross_reference: WWF:AT1307
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1307

Oman and United Arab Emirates Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:54:57Z
database_cross_reference: WWF:AT1306
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1306
has_exact_synonym: Arabian Peninsula: Oman and United Arab Emirates Ecoregion

Ethiopian Xeric Grasslands and Shrublands Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:08:06Z
database_cross_reference: WWF:AT1305
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1305

Eritrean Coastal Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:11:29Z
database_cross_reference: WWF:AT1304
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1304

East Saharan Montane Xeric Woodland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:13:33Z
database_cross_reference: WWF:AT1303
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1303
has_exact_synonym: North central Africa: Eastern Chad and small area of western Sudan

Oman, Yemen, and Saudi Arabia Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:16:12Z
database_cross_reference: WWF:AT1302
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1302
has_exact_synonym: Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion

Aldabra Island Xeric Scrub Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:18:09Z
database_cross_reference: WWF:AT1301
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1301

Indo-Malay Ecoregion
type: NamedIndividual
creation date: 2019-04-26T23:38:50Z
database_cross_reference: deserts-and-xeric-shrublands

Thar Desert
type: NamedIndividual
part of: Indo-Malay Ecoregion
creation date: 2019-04-26T23:40:13Z
database_cross_reference: im1304
database_cross_reference: WWF:IM1304
has_related_synonym: Southern Asia: Western India into Pakistan

Northwestern Thorn Scrub Forests
type: NamedIndividual
part of: Indo-Malay Ecoregion
creation date: 2019-04-27T00:12:51Z
database_cross_reference: im1303
database_cross_reference: WWF:IM1303
has_related_synonym: Southern Asia: Eastern India and western Pakistan

Solar radiation
type: NamedIndividual
process has causal agent: Q525
definition: Stellar radiation emitted from Sol.

example to be eventually removed
type: NamedIndividual
IAO_0000111: example to be eventually removed

metadata complete
type: NamedIndividual
IAO_0000111: 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
IAO_0000111: organizational term
definition: The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.

ready for release
type: NamedIndividual
IAO_0000111: ready for release
IAO_0000114: 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
IAO_0000111: 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
IAO_0000111: 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
IAO_0000111: 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
IAO_0000111: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
IAO_0000111: requires discussion
IAO_0000114: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

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: GO_0003674
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: GO_0003674
  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: GO_0003674
  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: GO_0008150
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

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

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

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

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

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

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

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

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

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y