gorel.owl
type: Ontology
description: This ontology combines RO together with GO-specific relations in the GOREL namespace, used for annotation extensions. See; Huntley, R. P., Harris, M. a, Alam-Faruque, Y., et al (2014). A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics, 15(1), 155. doi:10.1186/1471-2105-15-155 Notes on release edition (gorel.owl): This ontology is created by merging the relevant subset of RO together with GO-specific annotations of RO relations, and GOREL relations Notes on editors version (gorel-edit.owl): The editors version imports ro.owl, and allows addition of new relations (GOREL ID space) and annotation of existing RO relations. Note for editors: if an RO relation is to be made visible in the final gorel product, then make the relation a SubProperty of 'go annotation extension relation'. Anything with a logical axiom is included in the final module. Consult Makefile for details
default-namespace: external
comment: Includes Ontology(OntologyID(Anonymous-3)) [Axioms: 2177 Logical Axioms: 520]

definition
type: AnnotationProperty

term replaced by
type: AnnotationProperty

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.

display label for users
type: AnnotationProperty
sub property of: synonym_type_property

AE biological process
type: AnnotationProperty
comment: GO biological process
sub property of: subset_property

AE cell or anatomical
type: AnnotationProperty
comment: cell or anatomical
sub property of: subset_property

AE cellular component
type: AnnotationProperty
comment: GO cellular component
sub property of: subset_property

AE chemical
type: AnnotationProperty
comment: Chemical
sub property of: subset_property

AE developmental stages
type: AnnotationProperty
comment: Developmental stages
sub property of: subset_property

AE molecular function
type: AnnotationProperty
comment: GO molecular function
sub property of: subset_property

AE sequence feature
type: AnnotationProperty
comment: Sequence feature
sub property of: subset_property

AE sequence or complex
type: AnnotationProperty
comment: Protein, protein complex, gene or transcript identifier
sub property of: subset_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
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: generically dependent continuant
local domain: BFO:0000001
local range: CL:0000000 GO:0005575 GO:0008150 PO:0009012 PO:0025131 UBERON:0001062 ZFS:0100000 WBls:0000075 WBbt:0004017 WBbt:0005766 NCBITaxon:1 FBbt:10000000 FBdv:00007012 FBbt:00007002 EMAPA:0 ZFA:0100000
usage: This relation has two uses in annotation extension. It may be used to relate a cellular component to some cellular component, cell or anatomical structure that it is part of. It may also be used to relate a molecular function or biological process to a biological process or developmental stage of which it is a part. It may not be used to relate cellular components to functions, processes or stages, or to relate processes or functions to cellular components, cells or anatomical structures.
database_cross_reference: BFO:0000050
has_exact_synonym: part of
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: AE developmental stages
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: part_of

Axiom
annotated source: part of
annotated property: has_exact_synonym
annotated target: part of
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
RO_0001900: RO_0001901
database_cross_reference: BFO:0000051
has_exact_synonym: has part
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: has_part

Axiom
annotated source: has part
annotated property: has_exact_synonym
annotated target: has part
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
IAO_0000111: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
database_cross_reference: BFO:0000062
in_subset: ro-eco
shorthand: preceded_by

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.
database_cross_reference: BFO:0000063
in_subset: ro-eco
shorthand: precedes

occurs in
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1 FBbt:10000000 FBbt:00007002 ZFA:0100000
usage: Identifies the cell, tissue, cellular component or anatomical entity within which all parts of the molecular function or biological process occurs
database_cross_reference: BFO:0000066
has_obo_namespace: go/extensions/gorel
has_related_synonym: in
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: occurs_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
comment: Previous definition "p occurs_in c if and only if all of the participants of p are part_of c." [BFO:cjm]

Axiom
annotated source: occurs in
annotated property: has_related_synonym
annotated target: in
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

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
database_cross_reference: BFO:0000067
shorthand: contains_process
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

go annotation extension relation
type: ObjectProperty
database_cross_reference: GOREL:0000000
shorthand: go_annotation_extension_relation

during
type: ObjectProperty
type: TransitiveProperty
range: process
local domain: BFO:0000015
local range: BFO:0000007 WBls:0000075 ZFS:0100000
usage: Identifies a process or life stage during which a molecular function or biological process occurs or a cellular component is present
database_cross_reference: GOREL:0000002
has_obo_namespace: go/extensions/gorel
shorthand: during

obsolete localizes_to
type: ObjectProperty
domain: independent continuant
property chain axiom: part of
definition: OBSOLETE. c localizes_to d if c executes some function when it is part_of d.
local domain: BFO:0000004
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
usage: OBSOLETE. c localizes_to d if c executes some function when it is part_of d.
database_cross_reference: GOREL:0000003
has_exact_synonym: localization_destination
has_obo_namespace: go/extensions/gorel
shorthand: localizes_to
comment: TODO : check this one. Note Pombe is using different variant.
deprecated: true

Axiom
annotated source: obsolete localizes_to
annotated property: definition
annotated target: OBSOLETE. c localizes_to d if c executes some function when it is part_of d.
database_cross_reference: BFO:cjm

Axiom
annotated source: obsolete localizes_to
annotated property: has_exact_synonym
annotated target: localization_destination
database_cross_reference: GOC:mah

obsolete dependent_on
type: ObjectProperty
definition: OBSOLETE. Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
usage: Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
database_cross_reference: GOREL:0000004
has_exact_synonym: dependent on
has_obo_namespace: go/extensions/gorel
shorthand: dependent_on
comment: PomBase uses the more specific child relations, and avoids using dependent_on directly.
deprecated: true

Axiom
annotated source: obsolete dependent_on
annotated property: definition
annotated target: OBSOLETE. Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
database_cross_reference: GOC:rph

Axiom
annotated source: obsolete dependent_on
annotated property: has_exact_synonym
annotated target: dependent on
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete has_target_cell
type: ObjectProperty
domain: BFO_0000001
range: cell
definition: OBSOLETE. Was not defined before obsoletion.
local domain: BFO:0000001
local range: CL:0000000 WBbt:0004017
consider: has_input
consider: has_output
database_cross_reference: GOREL:0000006
has_obo_namespace: go/extensions/gorel
shorthand: has_target_cell
comment: this relation has been obsoleted it was unclear whether the associated cell type id should correspond to the final mature or precursor cell. If the outcome of a process is a modified cell, then the relationships has_output or has_input along with a CL identifier respectively defining the precursor or mature cell type can be considered instead.
deprecated: true

obsolete has_target_anatomical_entity
type: ObjectProperty
domain: BFO_0000001
range: CARO_0000000
definition: OBSOLETE. Was not defined before obsoletion.
local domain: BFO:0000001
local range: CARO:0000000
consider: has_input
consider: has_output
database_cross_reference: GOREL:0000007
has_obo_namespace: go/extensions/gorel
shorthand: has_target_anatomical_entity
comment: this relation has been obsoleted it was unclear whether the associated anatomical entity id should correspond to the final form or precursor anatomical entity. If the outcome of a process is a modified anatomical entity, then relationships has_output or has_input along with a anatomy identifier respectively defining the precursor or mature anatomical entity id can be considered instead.
deprecated: true

obsolete localization_dependent_on
type: ObjectProperty
domain: GO_0005575
definition: OBSOLETE. Identifies a requirement under which the gene product is located at the specified cellular component.
usage: Identifies a requirement under which the gene product is located at the specified cellular component.
database_cross_reference: GOREL:0000009
has_exact_synonym: localized by
has_obo_namespace: go/extensions/gorel
shorthand: localization_dependent_on
comment: Previous definition "Located at CC only if (BP occurs) OR (feature is present in annotated gene product) OR (CC is present) OR (gene product is present)" [GOC:mah]
deprecated: true

Axiom
annotated source: obsolete localization_dependent_on
annotated property: definition
annotated target: OBSOLETE. Identifies a requirement under which the gene product is located at the specified cellular component.
database_cross_reference: GOC:rph

Axiom
annotated source: obsolete localization_dependent_on
annotated property: has_exact_synonym
annotated target: localized by
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete requires_sequence_feature
type: ObjectProperty
domain: BFO_0000007
range: SO_0000110
definition: OBSOLETE. A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in Molecular Function or Biological Process.
usage: A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in Molecular Function or Biological Process.
has_broad_synonym: requires
has_broad_synonym: requires_feature
database_cross_reference: GOREL:0000010
has_obo_namespace: go/extensions/gorel
shorthand: requires_sequence_feature
comment: strictly speaking, these fall outside the scope of GO, even with extended annotations
deprecated: true

Axiom
annotated source: obsolete requires_sequence_feature
annotated property: definition
annotated target: OBSOLETE. A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in Molecular Function or Biological Process.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_sequence_feature
annotated property: has_broad_synonym
annotated target: requires
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

Axiom
annotated source: obsolete requires_sequence_feature
annotated property: has_broad_synonym
annotated target: requires_feature
database_cross_reference: GOC:mah

obsolete requires_regulator
type: ObjectProperty
domain: BFO_0000007
definition: OBSOLETE. Annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process.
usage: annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process
has_broad_synonym: requires
database_cross_reference: GOREL:0000011
has_obo_namespace: go/extensions/gorel
shorthand: requires_regulator
deprecated: true

Axiom
annotated source: obsolete requires_regulator
annotated property: definition
annotated target: OBSOLETE. Annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_regulator
annotated property: has_broad_synonym
annotated target: requires
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete requires_substance
type: ObjectProperty
domain: BFO_0000007
range: CHEBI_24431
definition: OBSOLETE. The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance
usage: The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance
has_broad_synonym: requires
database_cross_reference: GOREL:0000012
has_obo_namespace: go/extensions/gorel
shorthand: requires_substance
deprecated: true

Axiom
annotated source: obsolete requires_substance
annotated property: definition
annotated target: OBSOLETE. The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_substance
annotated property: has_broad_synonym
annotated target: requires
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

independent_of
type: ObjectProperty
domain: BFO_0000001
definition: Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.
local domain: BFO:0000001
local range: CHEBI:24431 GO:0003674 GO:0005575 GO:0008150 GO:0032991 MI:0315 MOD:00000 PR:000000001 SO:0000110 SO:0000673 SO:0000704
usage: Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.
has_alternative_id: not_dependent_on
database_cross_reference: GOREL:0000013
has_exact_synonym: independent_of
has_exact_synonym: not dependent on
has_obo_namespace: go/extensions/gorel
in_subset: AE biological process
in_subset: AE chemical
in_subset: AE molecular function
in_subset: AE sequence feature
in_subset: AE sequence or complex
shorthand: independent_of
comment: DEPRECATION WARNING: The GO editors have agreed that this relation should be deprecated. There are two main reasons for this 1. The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation is true. This can not be expressed in OWL. Annotation extensions using this relation will never fold. 2. The relation includes a hidden negation. This is problematic for a number of reasons, the most important of which is that burying negations in otherwise positive relationships can cause serious problems for inference.

Axiom
annotated source: independent_of
annotated property: definition
annotated target: Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.
database_cross_reference: GOA:rph

Axiom
annotated source: independent_of
annotated property: has_exact_synonym
annotated target: independent_of
database_cross_reference: GOC:rph

Axiom
annotated source: independent_of
annotated property: has_exact_synonym
annotated target: not dependent on
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete inhibits_protease
type: ObjectProperty
domain: GO_0010466
definition: OBSOLETE. Identifies a specific target of regulation of a MF
local domain: GO:0010466
local range: PR:000000001 SO:0000673
usage: OBSOLETE. Identifies a specific target of regulation of a MF
database_cross_reference: GOREL:0000014
has_obo_namespace: go/extensions/gorel
shorthand: inhibits_protease
comment: This relation was made obsolete because it is undesirably specific and redundant with any GO term that would be used in col5. Annotations that used this might use a different, to-be-added, child of has_regulation_target that captures something about directness; this one would probably be direct.
deprecated: true

Axiom
annotated source: obsolete inhibits_protease
annotated property: definition
annotated target: OBSOLETE. Identifies a specific target of regulation of a MF
database_cross_reference: GOC:mah

obsolete has_regulation_target
type: ObjectProperty
property chain axiom: regulates
property chain axiom: has participant
database_cross_reference: GOREL:0000015
shorthand: obsolete_has_regulation_target
comment: This term was deprecated in favor or 'has input' or 'has primary input'.
deprecated: true

obsolete protease_activator
type: ObjectProperty
domain: GO_0010952
definition: OBSOLETE. Identifies a specific target of regulation of a MF
local domain: GO:0010952
local range: PR:000000001 SO:0000673
usage: OBSOLETE. Identifies a specific target of regulation of a MF
database_cross_reference: GOREL:0000017
has_obo_namespace: go/extensions/gorel
shorthand: protease_activator
comment: This relation was made obsolete because it is undesirably specific and redundant with any GO term that would be used in col5. Annotations that used this might use a different, to-be-added, child of has_regulation_target that captures something about directness; this one would be direct.
deprecated: true

Axiom
annotated source: obsolete protease_activator
annotated property: definition
annotated target: OBSOLETE. Identifies a specific target of regulation of a MF
database_cross_reference: GOC:mah

obsolete stabilizes
type: ObjectProperty
definition: OBSOLETE. Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)
usage: Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)
database_cross_reference: GOREL:0000018
has_exact_synonym: stabilizes
has_obo_namespace: go/extensions/gorel
shorthand: stabilizes
comment: Obsoleted, see https://github.com/geneontology/go-ontology/issues/18540.
deprecated: true

Axiom
annotated source: obsolete stabilizes
annotated property: definition
annotated target: OBSOLETE. Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete stabilizes
annotated property: has_exact_synonym
annotated target: stabilizes
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete has_upstream_or_downstream_target
type: ObjectProperty
domain: GO_0008150
definition: OBSOLETE. Was not defined before obsoletion.
local domain: GO:0008150
local range: GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
database_cross_reference: GOREL:0000020
has_obo_namespace: go/extensions/gorel
shorthand: has_upstream_or_downstream_target
deprecated: true

obsolete has_upstream_target
type: ObjectProperty
domain: GO_0008150
definition: OBSOLETE. Was not defined before obsoletion.
local domain: GO:0008150
local range: GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
database_cross_reference: GOREL:0000021
has_obo_namespace: go/extensions/gorel
shorthand: has_upstream_target
deprecated: true

obsolete has_downstream_target
type: ObjectProperty
definition: OBSOLETE. Was not defined before obsoletion.
local range: GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
database_cross_reference: GOREL:0000022
has_obo_namespace: go/extensions/gorel
shorthand: has_downstream_target
deprecated: true

obsolete transcriptionally_regulates
type: ObjectProperty
domain: GO_0006355
definition: OBSOLETE. Identifies gene whose transcription is regulated
term replaced by: has_regulation_target
local domain: GO:0006355
usage: OBSOLETE. Identifies gene whose transcription is regulated
database_cross_reference: GOREL:0000023
has_obo_namespace: go/extensions/gorel
shorthand: transcriptionally_regulates
comment: This relation was made obsolete because it is undesirably specific and redundant with any GO term that would be used in col5. Annotations that used this might use a different, to-be-added, child of has_regulation_target that captures something about directness; this one would be indirect.
deprecated: true

Axiom
annotated source: obsolete transcriptionally_regulates
annotated property: definition
annotated target: OBSOLETE. Identifies gene whose transcription is regulated
database_cross_reference: GOC:mah

obsolete not_during
type: ObjectProperty
definition: OBSOLETE. A BP during which an annotation does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
local domain: BFO:0000001
local range: BFO:0000007 WBls:0000075 ZFS:0100000
usage: A BP during which an annotation does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
has_broad_synonym: except during
database_cross_reference: GOREL:0000024
has_obo_namespace: go/extensions/gorel
is class level: true
shorthand: not_during
comment: This relation was obsoleted because GO-CAM specifications does not allow negative relations.
comment: domain can be any process or object or even quality
deprecated: true

Axiom
annotated source: obsolete not_during
annotated property: definition
annotated target: OBSOLETE. A BP during which an annotation does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete not_during
annotated property: has_broad_synonym
annotated target: except during
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete not_happens_during
type: ObjectProperty
definition: OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Molecular Function or Biological Process does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases).
local domain: BFO:0000007
local range: BFO:0000007 WBls:0000075 ZFS:0100000
usage: A Molecular Function or Biological Process during which an annotation to a Molecular Function or Biological Process does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases).
has_broad_synonym: except during
database_cross_reference: GOREL:0000025
has_exact_synonym: does_not_happen_during
has_exact_synonym: not_occurs_during
has_obo_namespace: go/extensions/gorel
is class level: true
shorthand: not_happens_during
comment: This relation was obsoleted because GO-CAM specifications does not allow negative relations.
deprecated: true

Axiom
annotated source: obsolete not_happens_during
annotated property: definition
annotated target: OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Molecular Function or Biological Process does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases).
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete not_happens_during
annotated property: has_broad_synonym
annotated target: except during
database_cross_reference: PomBase:curators

Axiom
annotated source: obsolete not_happens_during
annotated property: has_exact_synonym
annotated target: does_not_happen_during
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete not_happens_during
annotated property: has_exact_synonym
annotated target: not_occurs_during
database_cross_reference: GOC:mah

obsolete not_exists_during
type: ObjectProperty
definition: OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Cellular Component does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
local domain: BFO:0000004
local range: BFO:0000007 WBls:0000075 ZFS:0100000
usage: A Molecular Function or Biological Process during which an annotation to a Cellular Component does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
has_broad_synonym: except during
database_cross_reference: GOREL:0000026
has_exact_synonym: does_not_exist_during
has_obo_namespace: go/extensions/gorel
is class level: true
shorthand: not_exists_during
comment: This relation was obsoleted because GO-CAM specifications does not allow negative relations.
deprecated: true

Axiom
annotated source: obsolete not_exists_during
annotated property: definition
annotated target: OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Cellular Component does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete not_exists_during
annotated property: has_broad_synonym
annotated target: except during
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

Axiom
annotated source: obsolete not_exists_during
annotated property: has_exact_synonym
annotated target: does_not_exist_during
database_cross_reference: GOC:mah

obsolete in_presence_of
type: ObjectProperty
definition: OBSOLETE. Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
local domain: BFO:0000001
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
usage: Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
database_cross_reference: GOREL:0000027
has_exact_synonym: in presence of
has_obo_namespace: go/extensions/gorel
shorthand: in_presence_of
comment: This relation was obsoleted because it does not follow GO-CAM specifications.
deprecated: true

Axiom
annotated source: obsolete in_presence_of
annotated property: definition
annotated target: OBSOLETE. Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete in_presence_of
annotated property: has_exact_synonym
annotated target: in presence of
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete requires_localization
type: ObjectProperty
domain: GO_0008150
range: GO_0005575
definition: OBSOLETE. The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component
usage: The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component
database_cross_reference: GOREL:0000028
has_exact_synonym: dependent_on_localization
has_exact_synonym: only when located at
has_obo_namespace: go/extensions/gorel
shorthand: requires_localization
deprecated: true

Axiom
annotated source: obsolete requires_localization
annotated property: definition
annotated target: OBSOLETE. The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_localization
annotated property: has_exact_synonym
annotated target: dependent_on_localization
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_localization
annotated property: has_exact_synonym
annotated target: only when located at
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete requires_regulation_by
type: ObjectProperty
domain: BFO_0000007
definition: OBSOLETE. Was not defined before obsoletion. Annotated gene product participates in Biological Process or executes Molecular Function activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)
local domain: BFO:0000007
local range: GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
usage: annotated gene product participates in Biological Process or executes Molecular Function activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)
database_cross_reference: GOREL:0000029
has_exact_synonym: requires regulation by
has_obo_namespace: go/extensions/gorel
shorthand: requires_regulation_by
deprecated: true

Axiom
annotated source: obsolete requires_regulation_by
annotated property: definition
annotated target: OBSOLETE. Was not defined before obsoletion. Annotated gene product participates in Biological Process or executes Molecular Function activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_regulation_by
annotated property: has_exact_synonym
annotated target: requires regulation by
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete modified_by
type: ObjectProperty
definition: OBSOLETE. Identifies the gene product that catalyzes a modification on the annotated gene product
local domain: MOD:00000
local range: GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
usage: Identifies the gene product that catalyzes a modification on the annotated gene product
database_cross_reference: GOREL:0000030
has_exact_synonym: modified by
has_obo_namespace: go/extensions/gorel
shorthand: modified_by
comment: http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation
deprecated: true

Axiom
annotated source: obsolete modified_by
annotated property: definition
annotated target: OBSOLETE. Identifies the gene product that catalyzes a modification on the annotated gene product
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete modified_by
annotated property: has_exact_synonym
annotated target: modified by
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete condition
type: ObjectProperty
definition: OBSOLETE. Identifies a condition under which the ontology term is observed to apply to the annotated gene product
usage: Identifies a condition under which the ontology term is observed to apply to the annotated gene product
database_cross_reference: GOREL:0000031
has_exact_synonym: assay_condition
has_exact_synonym: under_condition
has_obo_namespace: go/extensions/gorel
shorthand: condition
deprecated: true

Axiom
annotated source: obsolete condition
annotated property: definition
annotated target: OBSOLETE. Identifies a condition under which the ontology term is observed to apply to the annotated gene product
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete condition
annotated property: has_exact_synonym
annotated target: assay_condition
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete condition
annotated property: has_exact_synonym
annotated target: under_condition
database_cross_reference: GOC:mah

exists_during
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: during
domain: independent continuant
range: process
local domain: BFO:0000004
local range: GO:0008150 WBls:0000075 ZFS:0100000 FBdv:00007012
usage: Identifies a process or life stage during which a cellular component is present
has_broad_synonym: during
database_cross_reference: GOREL:0000032
has_obo_namespace: go/extensions/gorel
in_subset: AE biological process
in_subset: AE developmental stages
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: exists_during
comment: Previous definition "c exists_during p if and only if the temporal extent bounded by the start and end of c is part_of the temporal extent of p." [BFO:cjm]

Axiom
annotated source: exists_during
annotated property: has_broad_synonym
annotated target: during
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete requires_direct_regulator
type: ObjectProperty
domain: GO_0003674
definition: Annotated gene product requires direct regulation by the gene product or complex identified in the extension. Includes cases where the annotated gene product is a catalytic subunit of a complex and requires a regulatory subunit for activity as well as cases where the regulator acts directly but interacts transiently.
usage: Annotated gene product requires direct regulation by the gene product or complex identified in the extension. Includes cases where the annotated gene product is a catalytic subunit of a complex and requires a regulatory subunit for activity as well as cases where the regulator acts directly but interacts transiently.
database_cross_reference: GOREL:0000033
has_exact_synonym: requires direct regulation by
has_obo_namespace: go/extensions/gorel
shorthand: requires_direct_regulator
comment: the gene product in the extension should be annotated to a "regulator" MF (implying that it acts directly to regulate the annotated gp activity)
deprecated: true

Axiom
annotated source: obsolete requires_direct_regulator
annotated property: definition
annotated target: Annotated gene product requires direct regulation by the gene product or complex identified in the extension. Includes cases where the annotated gene product is a catalytic subunit of a complex and requires a regulatory subunit for activity as well as cases where the regulator acts directly but interacts transiently.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_direct_regulator
annotated property: has_exact_synonym
annotated target: requires direct regulation by
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

regulates_o_transports_or_maintains_localization_of
type: ObjectProperty
range: continuant
created by: pg
creation date: 2020-08-28T07:03:28Z
database_cross_reference: GOREL:0000038
shorthand: regulates_o_transports_or_maintains_localization_of

obsolete occurs at
type: ObjectProperty
usage: Identifies the Cellular Component or sequence feature adjacent to or in the vicinity of which the Molecular Function or Biological Process is executed
database_cross_reference: GOREL:0000501
has_related_synonym: at
shorthand: occurs_at
comment: Previous definition "P occurs_at C : the execution of P is located at C." [GOC:cjm, GOC:mah] This relation is not constrained with respect to whether C completely surrounds, or is adjacent to, the location where P is executed. Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin.
deprecated: true

Axiom
annotated source: obsolete occurs at
annotated property: has_related_synonym
annotated target: at
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete requires_modification
type: ObjectProperty
domain: BFO_0000007
range: MOD_00000
definition: OBSOLETE. Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.
usage: Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.
database_cross_reference: GOREL:0000502
has_exact_synonym: only with modification
has_obo_namespace: go/extensions/gorel
shorthand: requires_modification
comment: Note this relation is not intended for use in GO annotation. Discussion about using PR ID in column 17 instead; if we agree on that, this relation will be made obsolete
deprecated: true

Axiom
annotated source: obsolete requires_modification
annotated property: definition
annotated target: OBSOLETE. Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete requires_modification
annotated property: has_exact_synonym
annotated target: only with modification
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete not_occurs_in
type: ObjectProperty
definition: OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) in which a Biological Process or Molecular Function does not occur. Opposite of occurs_in.
local domain: BFO:0000007
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
usage: An entity (e.g. Cellular Component, cell type or anatomical entity) in which a Biological Process or Molecular Function does not occur. Opposite of occurs_in.
database_cross_reference: GOREL:0000506
has_obo_namespace: go/extensions/gorel
has_related_synonym: not in
is class level: true
shorthand: not_occurs_in
comment: This relation was obsoleted because GO-CAM specifications does not allow negative relations.
deprecated: true

Axiom
annotated source: obsolete not_occurs_in
annotated property: definition
annotated target: OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) in which a Biological Process or Molecular Function does not occur. Opposite of occurs_in.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete not_occurs_in
annotated property: has_related_synonym
annotated target: not in
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

activated_by
type: ObjectProperty
usage: Identifies a chemical substance that increases the activity of the gene product.
database_cross_reference: GOREL:0000507
has_exact_synonym: activated by
has_exact_synonym: activated_by_chemical
has_exact_synonym: activated_by_substance
has_exact_synonym: activity_increased_by
has_obo_namespace: go/extensions/gorel
shorthand: activated_by
comment: This relation should not be used to annotate one gene product regulating another's activity; a regulator MF or regulation BP should be used in such cases.

Axiom
annotated source: activated_by
annotated property: has_exact_synonym
annotated target: activated by
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

Axiom
annotated source: activated_by
annotated property: has_exact_synonym
annotated target: activated_by_chemical
database_cross_reference: GOC:mah

Axiom
annotated source: activated_by
annotated property: has_exact_synonym
annotated target: activated_by_substance
database_cross_reference: GOC:mah

Axiom
annotated source: activated_by
annotated property: has_exact_synonym
annotated target: activity_increased_by
database_cross_reference: GOC:mah

inhibited_by
type: ObjectProperty
definition: Identifies a chemical substance that decreases the activity of the gene product.
usage: Identifies a chemical substance that decreases the activity of the gene product.
database_cross_reference: GOREL:0000508
has_exact_synonym: activity_decreased_by
has_exact_synonym: inhibited by
has_exact_synonym: inhibited_by_chemical
has_exact_synonym: inhibited_by_substance
has_obo_namespace: go/extensions/gorel
shorthand: inhibited_by
comment: This relation should not be used to annotate one gene product regulating another's activity; a regulator MF or regulation BP should be used in such cases.

Axiom
annotated source: inhibited_by
annotated property: definition
annotated target: Identifies a chemical substance that decreases the activity of the gene product.
database_cross_reference: GOC:mah

Axiom
annotated source: inhibited_by
annotated property: has_exact_synonym
annotated target: activity_decreased_by
database_cross_reference: GOC:mah

Axiom
annotated source: inhibited_by
annotated property: has_exact_synonym
annotated target: inhibited by
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

Axiom
annotated source: inhibited_by
annotated property: has_exact_synonym
annotated target: inhibited_by_chemical
database_cross_reference: GOC:mah

Axiom
annotated source: inhibited_by
annotated property: has_exact_synonym
annotated target: inhibited_by_substance
database_cross_reference: GOC:mah

obsolete not_occurs_at
type: ObjectProperty
definition: OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.
local domain: BFO:0000007
local range: GO:0005575 SO:0000110
usage: An entity (e.g. Cellular Component, sequence feature) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.
database_cross_reference: GOREL:0000509
has_obo_namespace: go/extensions/gorel
has_related_synonym: not at
is class level: true
shorthand: not_occurs_at
comment: This relation was obsoleted because GO-CAM specifications does not allow negative relations.
deprecated: true

Axiom
annotated source: obsolete not_occurs_at
annotated property: definition
annotated target: OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.
database_cross_reference: GOC:mah

Axiom
annotated source: obsolete not_occurs_at
annotated property: has_related_synonym
annotated target: not at
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete has_indirect_input
type: ObjectProperty
definition: OBSOLETE. Was not defined before obsoletion.
local domain: BFO:0000007
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
usage: Identifies an entity indirectly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in MF or BP.
has_alternative_id: GOREL:0000505
has_alternative_id: has_indirect_target
has_alternative_id: indirectly_localizes
database_cross_reference: GOREL:0000751
has_exact_synonym: has_indirect_target
has_narrow_synonym: indirectly_localizes
has_obo_namespace: go/extensions/gorel
shorthand: has_indirect_input
comment: If the entity is directly bound/acted upon by the gene product that is the subject of the annotation, then the relation: has_direct_input should be alternatively considered. [GOC:ecd]
deprecated: true

Axiom
annotated source: obsolete has_indirect_input
annotated property: has_exact_synonym
annotated target: has_indirect_target
database_cross_reference: GOC:ecd

Axiom
annotated source: obsolete has_indirect_input
annotated property: has_narrow_synonym
annotated target: indirectly_localizes
database_cross_reference: GOC:ecd

obsolete has_direct_input
type: ObjectProperty
local domain: BFO:0000015
usage: Identifies an entity directly affected (transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process. It is expected that the gene product and entity will physically interact, this can be determined either by a direct binding assay or inferred from the activity of the gene product, for example, a gene product with catalytic activity is inferred to bind its substrate.
has_alternative_id: GOREL:0000019
has_alternative_id: GOREL:0000504
has_alternative_id: directly_localizes
has_alternative_id: has_direct_target
has_alternative_id: has_substrate
database_cross_reference: GOREL:0000752
has_exact_synonym: has_direct_target
has_narrow_synonym: directly_localizes
has_narrow_synonym: has_substrate
has_obo_namespace: go/extensions/gorel
shorthand: has_direct_input
comment: If the entity is indirectly bound/acted upon by the gene product that is the subject of an annotation, then the relation: has_indirect_input should be considered [GOC:ecd]
comment: This relation is part of the ShEx speficications.
deprecated: true

Axiom
annotated source: obsolete has_direct_input
annotated property: has_exact_synonym
annotated target: has_direct_target
database_cross_reference: GOC:ecd

Axiom
annotated source: obsolete has_direct_input
annotated property: has_narrow_synonym
annotated target: directly_localizes
database_cross_reference: GOC:ecd

Axiom
annotated source: obsolete has_direct_input
annotated property: has_narrow_synonym
annotated target: has_substrate
database_cross_reference: GOC:ecd

obsolete requires_target_sequence_feature
type: ObjectProperty
domain: BFO_0000001
range: SO_0000110
definition: OBSOLETE. Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process
local domain: BFO:0000001
local range: SO:0000110
usage: Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process
database_cross_reference: GOREL:0000754
has_exact_synonym: requires feature in target
has_obo_namespace: go/extensions/gorel
shorthand: requires_target_sequence_feature
deprecated: true

Axiom
annotated source: obsolete requires_target_sequence_feature
annotated property: definition
annotated target: OBSOLETE. Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process
database_cross_reference: GOC:ecd

Axiom
annotated source: obsolete requires_target_sequence_feature
annotated property: has_exact_synonym
annotated target: requires feature in target
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

obsolete in_absence_of
type: ObjectProperty
definition: OBSOLETE. Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
local domain: BFO:0000001
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
usage: Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
database_cross_reference: GOREL:0000755
has_obo_namespace: go/extensions/gorel
shorthand: in_absence_of
comment: DEPRECATION WARNING: The GO editors have agreed that this relation should be deprecated. There are two main reasons for this 1. The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation is true. This can not be expressed in OWL. Annotation extensions using this relation will never fold. 2. The relation includes a hidden negation. This is problematic for a number of reasons, the most important of which is that burying negations in otherwise positive relationships can cause serious problems for inference.
comment: This relation was obsoleted because it does not follow GO-CAM specifications.
deprecated: true

Axiom
annotated source: obsolete in_absence_of
annotated property: definition
annotated target: OBSOLETE. Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
database_cross_reference: GOC:rph

axis_of
type: ObjectProperty
database_cross_reference: GOREL:0001000
has_obo_namespace: go/extensions/gorel
shorthand: axis_of

has_output_o_axis_of
type: ObjectProperty
property chain axiom: has output
property chain axiom: axis_of
definition: This is the combination of the has_output relation with the axis_of relation
usage: This is the combination of the has_output relation with the axis_of relation
database_cross_reference: GOREL:0001002
has_obo_namespace: go/extensions/gorel
shorthand: has_output_o_axis_of
comment: Example of use: anterior/posterior pattern specification has_output_o_axis_of lateral plate mesoderm. Note that the output of this process is an *axis*, not the LPM itself. This relation chain allows us to use an anatomical structure as the slot value

Axiom
annotated source: has_output_o_axis_of
annotated property: propertyChainAxiom
annotated target: has output
annotated target: axis_of
IAO is reversible property chain: true

Axiom
annotated source: has_output_o_axis_of
annotated property: definition
annotated target: This is the combination of the has_output relation with the axis_of relation
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:mtg_berkeley_2012_08_27

regulates_o_has_output
type: ObjectProperty
property chain axiom: regulates
property chain axiom: has output
definition: This is the combination of the regulates relation with the has_output relation
usage: This is the combination of the regulates relation with the has_output relation
database_cross_reference: GOREL:0001003
shorthand: regulates_o_has_output

Axiom
annotated source: regulates_o_has_output
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: has output
IAO is reversible property chain: true

Axiom
annotated source: regulates_o_has_output
annotated property: definition
annotated target: This is the combination of the regulates relation with the has_output relation
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:mtg_berkeley_2012_08_27

regulates process that occurs in
type: ObjectProperty
property chain axiom: regulates
property chain axiom: occurs in
IAO_0000112: 'negative regulation of chromosome segregation' that regulates_o_occurs_in some spermatocyte.
definition: A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.
usage: Use this relation to link a regulatory process or function to the structure that the regulated process or function occurs in.
database_cross_reference: GOREL:0001004
has_exact_synonym: regulates_o_occurs_in
has_obo_namespace: go/extensions/gorel
shorthand: regulates_o_occurs_in

Axiom
annotated source: regulates process that occurs in
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: occurs in
IAO is reversible property chain: true

Axiom
annotated source: regulates process that occurs in
annotated property: definition
annotated target: A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:mtg_berkeley_2012_08_27

regulates process that results in movement of
type: ObjectProperty
domain: GO_0040012
property chain axiom: regulates
property chain axiom: results in movement of
definition: A relation that holds between a process that regulates locomotion and the cell or organism whose locomotion is being regulated.
usage: Use this relation to relate a process that regulates locomotion to the cell or organism whose locomotion is being regulated.
database_cross_reference: GOREL:0001005
has_exact_synonym: regulates_o_results_in_movement_of
has_obo_namespace: go/extensions/gorel
shorthand: regulates_o_results_in_movement_of
comment: This is the combination of the regulates relation with the results_in_movement_of relation. Example of use: an annotation of gene X to 'regulation of cell migration with 'regulates_o_results_in_movement_of(CL:0000653) in column 16 would mean that gene X is involved in the regulation of glomerular visceral epithelial cell migration.

Axiom
annotated source: regulates process that results in movement of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in movement of
IAO is reversible property chain: true

Axiom
annotated source: regulates process that results in movement of
annotated property: definition
annotated target: A relation that holds between a process that regulates locomotion and the cell or organism whose locomotion is being regulated.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:mtg_berkeley_2012_08_27

obsolete acts_on_population_of
type: ObjectProperty
sub property of: has participant
domain: process
definition: OBSOLETE. The relationship that links an entity with a process in which the process has more than one participant that is of the same entity type.
term replaced by: RO:0012003
local domain: GO:0008283
local range: CL:0000000 WBbt:0004017
usage: Use this relation to relate a process to a population of cells that it acts on. The main usage of this relations is to relate GO: cell proliferation to the proliferating cells type. (Individual cells divide, populations of cells proliferate.)
has_broad_synonym: alters levels of
database_cross_reference: GOREL:0001006
database_cross_reference: RO:0012003
has_obo_namespace: go/extensions/gorel
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: acts_on_population_of
comment: Example of use: an annotation of gene X to cell proliferation with acts_on_population_of CL:0000057 means that gene X is involved in the proliferation of fibroblasts. Note that many annotation extensions use regulates_o_acts_on_population_of - should this be considered regulation of number of cells / cell homeostasis?
deprecated: true

Axiom
annotated source: obsolete acts_on_population_of
annotated property: definition
annotated target: OBSOLETE. The relationship that links an entity with a process in which the process has more than one participant that is of the same entity type.
database_cross_reference: GOC:mtg_berkeley_2013

obsolete mediated by
type: ObjectProperty
term replaced by: process has causal agent
created by: pg
creation date: 2019-11-21T19:16:04Z
database_cross_reference: GOREL:0001007
has_obo_namespace: go/extensions/gorel
id: mediated_by
shorthand: obsolete_mediated_by
deprecated: true

obsolete regulates process that acts on population of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: obsolete acts_on_population_of
IAO_0000112: 'positive regulation of cell proliferation' and 'regulates process that acts on population of' some 'stem cell'
definition: A relation that applies between a regulatory process and a population of entities that a process it regulates acts on.
usage: This is the combination of the regulates relation with the acts_on_population_of relation.
database_cross_reference: GOREL:0001008
has_exact_synonym: regulates_o_acts_on_population_of
has_obo_namespace: go/extensions/gorel
shorthand: regulates_o_acts_on_population_of
deprecated: true

Axiom
annotated source: obsolete regulates process that acts on population of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: obsolete acts_on_population_of
IAO is reversible property chain: true

Axiom
annotated source: obsolete regulates process that acts on population of
annotated property: definition
annotated target: A relation that applies between a regulatory process and a population of entities that a process it regulates acts on.
database_cross_reference: GOC:mtg_berkeley_2013

regulates acquisition of features of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: results in acquisition of features of
definition: This is the combination of the regulates relation with the results_in_acquisition_of_features_of relation.
usage: Use this relation to relate a process that regulates the differentiation of a cell type or anatomical structure to the specific cell type or anatomical structure in question.
database_cross_reference: GOREL:0001010
has_exact_synonym: regulates differentiation of
has_exact_synonym: regulates_o_results_in_acquisition_of_features_of
has_obo_namespace: go/extensions/gorel
shorthand: regulates_o_results_in_acquisition_of_features_of

Axiom
annotated source: regulates acquisition of features of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in acquisition of features of
IAO is reversible property chain: true

Axiom
annotated source: regulates acquisition of features of
annotated property: definition
annotated target: This is the combination of the regulates relation with the results_in_acquisition_of_features_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates_o_has_agent
type: ObjectProperty
range: independent continuant
property chain axiom: regulates
property chain axiom: obsolete has active participant
definition: A relationship between the regulation of a process and the agent that executes that process.
database_cross_reference: GOREL:0001011
has_exact_synonym: regulates_o_has_agent
shorthand: regulates_o_has_agent

Axiom
annotated source: regulates_o_has_agent
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: obsolete has active participant
IAO is reversible property chain: true

Axiom
annotated source: regulates_o_has_agent
annotated property: definition
annotated target: A relationship between the regulation of a process and the agent that executes that process.
database_cross_reference: GOC:dos

regulates maturation of
type: ObjectProperty
sub property of: go annotation extension relation
domain: process
property chain axiom: regulates
property chain axiom: results in maturation of
definition: This is the combination of the regulates relation with the results_in_maturation_of relation.
usage: This is the combination of the regulates relation with the results_in_maturation_of relation.
database_cross_reference: GOREL:0001012
shorthand: regulates_o_results_in_maturation_of

Axiom
annotated source: regulates maturation of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in maturation of
IAO is reversible property chain: true

Axiom
annotated source: regulates maturation of
annotated property: definition
annotated target: This is the combination of the regulates relation with the results_in_maturation_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates_o_has_participant
type: ObjectProperty
definition: This is the combination of the regulates relation with the has_participant relation.
usage: Use this relationship to link a regulatory process or function to an entity that participates in the regulated process.
database_cross_reference: GOREL:0001016
shorthand: regulates_o_has_participant

Axiom
annotated source: regulates_o_has_participant
annotated property: definition
annotated target: This is the combination of the regulates relation with the has_participant relation.
database_cross_reference: GOC:mtg_berkeley_2013

results_in_division_of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: has participant
domain: process
range: cell
definition: The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type.
local domain: BFO:0000015
local range: CL:0000000 WBbt:0004017 FBbt:00007002
usage: The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type.
database_cross_reference: GOREL:0001019
has_obo_namespace: go/extensions/gorel
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_division_of
comment: Example of use: an annotation of gene X to cell division with results_in_division_of CL:0000057 (fibroblast) means that at the end of the process a single fibroblast has divided into two fibroblasts.

Axiom
annotated source: results_in_division_of
annotated property: definition
annotated target: The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type.
database_cross_reference: GOC:mtg_berkeley_2013

regulates commitment to
type: ObjectProperty
range: cell
property chain axiom: regulates
property chain axiom: results in commitment to
definition: A relation that applies between a process that regulates cell fate commitment and the cell type that the regulated process results in commitment to.
usage: This is the combination of the regulates relation with the results_in_commitment_to relation.
database_cross_reference: GOREL:0001022
has_exact_synonym: regulates_o_results_in_commitment_to
shorthand: regulates_o_results_in_commitment_to

Axiom
annotated source: regulates commitment to
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in commitment to
IAO is reversible property chain: true

Axiom
annotated source: regulates commitment to
annotated property: definition
annotated target: A relation that applies between a process that regulates cell fate commitment and the cell type that the regulated process results in commitment to.
database_cross_reference: GOC:mtg_berkeley_2013

regulates development of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: results in development of
definition: This is the combination of the regulates relation with the results_in_development_of relation.
usage: Use this relation to relate 'regulation of developmental process' or one of its subclasses to the structure that the regulated developmental process results in the development of.
database_cross_reference: GOREL:0001023
has_exact_synonym: regulates_o_results_in_development_of
has_obo_namespace: go/extensions/gorel
shorthand: regulates_o_results_in_development_of

Axiom
annotated source: regulates development of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in development of
IAO is reversible property chain: true

Axiom
annotated source: regulates development of
annotated property: definition
annotated target: This is the combination of the regulates relation with the results_in_development_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates division of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: results_in_division_of
definition: This is the combination of the regulates relation with the results_in_division_of relation.
usage: This is the combination of the regulates relation with the results_in_division_of relation.
database_cross_reference: GOREL:0001024
shorthand: regulates_o_results_in_division_of

Axiom
annotated source: regulates division of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results_in_division_of
IAO is reversible property chain: true

Axiom
annotated source: regulates division of
annotated property: definition
annotated target: This is the combination of the regulates relation with the results_in_division_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates formation of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: results in formation of anatomical entity
definition: This is the combination of the regulates relation with the results_in_formation_of relation.
usage: This is the combination of the regulates relation with the results_in_formation_of relation.
database_cross_reference: GOREL:0001025
shorthand: regulates_o_results_in_formation_of

Axiom
annotated source: regulates formation of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in formation of anatomical entity
IAO is reversible property chain: true

Axiom
annotated source: regulates formation of
annotated property: definition
annotated target: This is the combination of the regulates relation with the results_in_formation_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates morphogenesis of
type: ObjectProperty
domain: GO_0050789
property chain axiom: regulates
property chain axiom: results in morphogenesis of
definition: This is the combination of the regulates relation with the results_in_morphogenesis_of relation.
usage: This is the combination of the regulates relation with the results_in_morphogenesis_of relation.
database_cross_reference: GOREL:0001026
shorthand: regulates_o_results_in_morphogenesis_of

Axiom
annotated source: regulates morphogenesis of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in morphogenesis of
IAO is reversible property chain: true

Axiom
annotated source: regulates morphogenesis of
annotated property: definition
annotated target: This is the combination of the regulates relation with the results_in_morphogenesis_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates specification of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: results in specification of
definition: A relation that applies between a process that regulates the specification of some cell type or structure and the specified cell type or structure.
usage: Use this relation to link a process that regulates the specification of some cell type of anatomical structure, and the structure or cell type specified.
database_cross_reference: GOREL:0001027
has_exact_synonym: regulates_o_results_in_specification_of
has_obo_namespace: go/extensions/gorel
shorthand: regulates_o_results_in_specification_of

Axiom
annotated source: regulates specification of
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: results in specification of
IAO is reversible property chain: true

Axiom
annotated source: regulates specification of
annotated property: definition
annotated target: A relation that applies between a process that regulates the specification of some cell type or structure and the specified cell type or structure.
database_cross_reference: GOC:mtg_berkeley_2013

has_output_o_product_of
type: ObjectProperty
domain: process
property chain axiom: has output
property chain axiom: gene product of
definition: This is the combination of the has_output relation with the gene_product_of relation.
local domain: BFO:0000015
local range: PR:000000001 SO:0000673
usage: This is the combination of the has_output relation with the results_in_specification_of relation.
database_cross_reference: GOREL:0001029
has_obo_namespace: go/extensions/gorel
shorthand: has_output_o_product_of

Axiom
annotated source: has_output_o_product_of
annotated property: propertyChainAxiom
annotated target: has output
annotated target: gene product of
IAO is reversible property chain: true

Axiom
annotated source: has_output_o_product_of
annotated property: definition
annotated target: This is the combination of the has_output relation with the gene_product_of relation.
database_cross_reference: GOC:mtg_berkeley_2013

regulates_o_has_input
type: ObjectProperty
property chain axiom: regulates
property chain axiom: has input
definition: This is the combination of the regulates relation with the has_input relation
usage: This is the combination of the regulates relation with the has_input relation
database_cross_reference: GOREL:0001030
shorthand: regulates_o_has_input

Axiom
annotated source: regulates_o_has_input
annotated property: propertyChainAxiom
annotated target: regulates
annotated target: has input
IAO is reversible property chain: true

Axiom
annotated source: regulates_o_has_input
annotated property: definition
annotated target: This is the combination of the regulates relation with the has_input relation
database_cross_reference: GOC:dph

obsolete has_intermediate
type: ObjectProperty
term replaced by: RO_0002505
created by: pg
creation date: 2019-11-21T16:32:15Z
database_cross_reference: GOREL:0002008
has_obo_namespace: go/extensions/gorel
shorthand: obsolete_has_intermediate
deprecated: true

obsolete results_in_transport_to_from_or_mediated_by
type: ObjectProperty
created by: pg
creation date: 2019-11-21T18:00:03Z
database_cross_reference: GOREL:0002010
has_obo_namespace: go/extensions/gorel
shorthand: obsolete_results_in_transport_to_from_or_mediated_by
comment: This relation was only used for one class, 'endosomal transport' (GO:0016197), which groups together disparate roles the participants can play - it was defined as 'The directed movement of substances into, out of *or mediated by* an endosome...' The term has been redefined and the logical definition changed accordingly.
deprecated: true

obsolete regulates activity of
type: ObjectProperty
definition: OBSOLETE. A relation that holds between the regulation of a molecular function and the agent that executes that function.
local domain: GO:0098772 GO:0065009
local range: GO:0032991 SO:0000374 PR:000000001
usage: Use this relation to link either a molecular function, or a biological process that regulates a molecular function, to the gene product or complex that executes the regulated function.
database_cross_reference: GOREL:0098702
shorthand: regulates_activity_of
comment: This relation has been obsoleted as it is not part of the GO ShEx specifications.
deprecated: true

obsolete regulates transcription of
type: ObjectProperty
definition: OBSOLETE. A relationship that holds between a process and a gene whose transcription is regulated by that process.
usage: Relates a regulatory process or function to the gene whose transcription it regulates.
database_cross_reference: GOREL:0098788
shorthand: regulates_transcription_of
comment: Usage of this relation has been deprecated in favor of 'has direct input'.
deprecated: true

Axiom
annotated source: obsolete regulates transcription of
annotated property: usage
annotated target: Relates a regulatory process or function to the gene whose transcription it regulates.
database_cross_reference: GOC:dos

obsolete regulates expression of
type: ObjectProperty
definition: OBSOLETE. A relationship that holds between a process and a gene whose expression is regulated by that process.
usage: Relates a regulatory process or function to the gene whose expression it regulates. Expression encompasses transcription, regulation and processing involved in maturation.
database_cross_reference: GOREL:0098789
shorthand: regulates_expression_of
comment: Usage of this relation has been deprecated in favor of 'has direct input'.
deprecated: true

Axiom
annotated source: obsolete regulates expression of
annotated property: usage
annotated target: Relates a regulatory process or function to the gene whose expression it regulates. Expression encompasses transcription, regulation and processing involved in maturation.
database_cross_reference: GOC:dos

obsolete regulates translation of
type: ObjectProperty
definition: OBSOLETE. A relationship that holds between a process and a protein coding gene whose translation is regulated by that process.
usage: Relates a regulatory process or function to the gene whose translation it regulates.
database_cross_reference: GOREL:0098790
shorthand: regulates_translation_of
comment: Regulation of translation includes processes that regulate the levels of mature mRNA available for translation, as well as direct regulation of the rate of translation.
comment: Usage of this relation has been deprecated in favor of 'has direct input'.
deprecated: true

Axiom
annotated source: obsolete regulates translation of
annotated property: usage
annotated target: Relates a regulatory process or function to the gene whose translation it regulates.
database_cross_reference: GOC:dos

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
database_cross_reference: RO:0000052
shorthand: characteristic_of
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
RO_0001900: RO_0001901
database_cross_reference: RO:0000053
shorthand: has_characteristic

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
database_cross_reference: RO:0000056
shorthand: participates_in

has participant
type: ObjectProperty
sub property of: go annotation extension relation
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
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
local domain: BFO:0000015
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CARO:0000000
usage: Identifies an entity affected by the gene product's participation in a molecular function or biological process
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
database_cross_reference: RO:0000057
has_obo_namespace: go/extensions/gorel
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: has_participant
comment: Do not use this relation directly

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
IAO_0000116: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
IAO_0000118: function_of
IAO_0000118: is function of
database_cross_reference: RO:0000079
shorthand: function_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000112: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
database_cross_reference: RO:0000080
shorthand: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
IAO_0000118: is role of
IAO_0000118: role_of
database_cross_reference: RO:0000081
shorthand: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
IAO_0000118: has_function
database_cross_reference: RO:0000085
shorthand: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000112: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
IAO_0000118: has_quality
database_cross_reference: RO:0000086
shorthand: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
IAO_0000118: has_role
database_cross_reference: RO:0000087
shorthand: 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
database_cross_reference: RO:0000091
shorthand: has_disposition

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
database_cross_reference: RO:0000092
in_subset: RO_0002259
shorthand: disposition_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.

coincident with
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: mereotopologically related to
domain: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: https://orcid.org/0000-0002-7073-9172
local domain: GO:0005575
local range: CHEBI:24431 SO:0000001 SO:0000704
usage: Use this relation to link a region of chromosome or chromatin to the sequence region that it contains. The sequence region may be a specific gene or some generic region referred to by a SO term.
database_cross_reference: RO:0002008
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: coincident_with
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 transport of
type: ObjectProperty
sub property of: directly regulates
property chain axiom: regulates
property chain axiom: transports or maintains localization of
definition: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
usage: Use this relation to link a process that regulates transport to the the entity being transported.
database_cross_reference: RO:0002011
in_subset: AE chemical
in_subset: ro-eco
shorthand: regulates_transport_of

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
database_cross_reference: RO:0002013
shorthand: has_regulatory_component_activity

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
database_cross_reference: RO:0002014
shorthand: has_negative_regulatory_component_activity
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
database_cross_reference: RO:0002015
shorthand: has_positive_regulatory_component_activity
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:44:33Z
database_cross_reference: RO:0002017
shorthand: has_component_activity
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
database_cross_reference: RO:0002018
shorthand: has_component_process

transports
type: ObjectProperty
sub property of: transports or maintains localization of
definition: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-20T17:11:08Z
database_cross_reference: RO:0002020
shorthand: transports

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
database_cross_reference: RO:0002022
shorthand: directly_regulated_by
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
database_cross_reference: RO:0002023
shorthand: directly_negatively_regulated_by

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
database_cross_reference: RO:0002024
shorthand: directly_positively_regulated_by

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
database_cross_reference: RO:0002025
shorthand: has_effector_activity
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
database_cross_reference: RO:0002084
in_subset: ro-eco
shorthand: during_which_ends
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
database_cross_reference: RO:0002085
shorthand: encompasses
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
database_cross_reference: RO:0002086
in_subset: ro-eco
shorthand: ends_after
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
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: starts_at_end_of
database_cross_reference: RO:0002087
shorthand: immediately_preceded_by
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
database_cross_reference: RO:0002088
in_subset: ro-eco
shorthand: during_which_starts
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
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
database_cross_reference: RO:0002090
in_subset: ro-eco
shorthand: immediately_precedes
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
database_cross_reference: RO:0002091
in_subset: ro-eco
shorthand: starts_during
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: go annotation extension relation
sub property of: during
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
local domain: BFO:0000015
local range: GO:0008150 WBls:0000075 ZFS:0100000 UBERON:0000105 FBdv:00007012
usage: Identifies a process or life stage during which a molecular function or biological process occurs. This is weaker than parthood. So, for example, various processes occur during gastrulation without being part of it.
has_broad_synonym: during
database_cross_reference: RO:0002092
has_exact_synonym: occurs_during
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE developmental stages
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: happens_during
comment: Previous definition "p happens_during q if and only if the temporal extent of p is part_of the temporal extent of q." Note that part_of between processes implies happens_during (we must use OWL to express this), but happens_during does not imply part_of. Note also that this relation holds between two processes. To link a physical entity to a process by duration, use exists_during. [BFO:cjm] Note that in order to express that part_of between processes implies during, we must use OWL.
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

Axiom
annotated source: happens during
annotated property: has_broad_synonym
annotated target: during
database_cross_reference: PomBase:curators
has_synonym_type: display label for users

Axiom
annotated source: happens during
annotated property: has_exact_synonym
annotated target: occurs_during
database_cross_reference: GOC:mah

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
database_cross_reference: RO:0002093
in_subset: ro-eco
shorthand: ends_during
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

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
database_cross_reference: RO:0002131
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco
shorthand: overlaps

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

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
database_cross_reference: RO:0002163
in_subset: ro-eco
shorthand: spatially_disjoint_from

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: pending final vetting
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
database_cross_reference: RO:0002180
in_subset: ro-eco
shorthand: has_component

gene product of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: genomically related to
inverse of: has gene product
domain: independent continuant
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: continuant
range: Class
  union of: generically dependent continuant
  union of: material entity
IAO_0000114: pending final vetting
definition: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
IAO_0000116: We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
local domain: BFO:0000004
local range: BFO:0000002
usage: x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x.
has_alternative_id: GOREL:0001028
database_cross_reference: RO:0002204
has_obo_namespace: go/extensions/gorel
shorthand: gene_product_of

has gene product
type: ObjectProperty
sub property of: genomically related to
domain: continuant
range: independent continuant
IAO_0000112: every HOTAIR lncRNA is the gene product of some HOXC gene
IAO_0000112: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
IAO_0000114: pending final vetting
definition: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002205
shorthand: has_gene_product

regulates
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
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
local domain: BFO:0000015
local range: BFO:0000015
database_cross_reference: RO:0002211
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: regulates

negatively regulates
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
local domain: BFO:0000015
local range: BFO:0000015
database_cross_reference: RO:0002212
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: negatively_regulates

positively regulates
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
local domain: BFO:0000015
local range: BFO:0000015
database_cross_reference: RO:0002213
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: positively_regulates

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)".
database_cross_reference: RO:0002215
in_subset: ro-eco
shorthand: capable_of

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
database_cross_reference: RO:0002216
shorthand: capable_of_part_of

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

obsolete has active participant
type: ObjectProperty
definition: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has agent
term replaced by: causal agent in process
local domain: GO:0008150
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
usage: Use this relation to link a process to an entity that carries out that process. The entity may be a cellular component, a cell type or an anatomical structure. Examples include recording a vesicle type that mediates a transport process, a cell type that is the agent of a secretion process or a cell adhesion process. Do not use this to extend a molecular function: The agents of molecular functions are gene products and complexes. Use of this relation with a molecular function therefore consistutes reverse annotation.
has_alternative_id: GOREL:0001007
database_cross_reference: RO:0002218
shorthand: has_agent
comment: Example of use: an annotation of gene X to cytokine production with has_agent of CL:0000057 (fibroblast) means that the fibroblast is producing the cytokine.
deprecated: true

adjacent to
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0001900: RO_0001901
local domain: GO:0005575
local range: GO:0005575 CL:0000000
database_cross_reference: RO:0002220
has_exact_synonym: adjacent to
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: adjacent_to

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.

Axiom
annotated source: adjacent to
annotated property: has_exact_synonym
annotated target: adjacent to
has_synonym_type: adjacent to

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
database_cross_reference: RO:0002222
in_subset: ro-eco
shorthand: temporally_related_to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has start location
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: has part that occurs in
domain: process
range: independent continuant
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
local domain: BFO:0000015
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1 FBbt:10000000 FBbt:00007002
usage: Use this relation to relate a biological process to its start location. Examples include recording the cell-type in which a cell-cell signaling process starts and recording a cellular compartment (such as post-synapse, presynapse or cilium) in which a signal transduction process starts. Note, if the entire process occurs in a particular location, use 'occurs in' instead.
database_cross_reference: RO:0002231
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: has_start_location

has end location
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: has part that occurs in
domain: process
range: independent continuant
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
local domain: BFO:0000015
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1
usage: Use this relation to relate a biological process to the location (cell component, cell type, anatomical location) in which the process ends. Examples include recording the cell-type or cellular compartment in which a cell-cell signalling process ends. To record a location in which the entire process occurs, please use 'occurs in'.
database_cross_reference: RO:0002232
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: has_end_location

has input
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: has participant
inverse of: input of
domain: process
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
local domain: BFO:0000015
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697 SO:0000839 SO:0001683 NCBITaxon:1
usage: Use this relation to relate a biological process or molecular function to an entity that participates in the process/function, is present at the start of the process/function and whose state is affected by that process/function. Change of state includes being transported, modified, consumed or destroyed. An input may be any continuant: chemical; gene product; cell component; cells type; organism. For inputs to MFs that are bound by the gene product that executes the MF, the more specific relation 'has_direct_input' may be used.
has_alternative_id: GOREL:0000016
has_alternative_id: GOREL:0000503
has_alternative_id: GOREL:0000753
has_alternative_id: has_target
has_alternative_id: localizes
database_cross_reference: GOREL:0000753
database_cross_reference: RO:0002233
has_exact_synonym: has_target
has_narrow_synonym: localizes
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE chemical
in_subset: AE sequence or complex
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: has_input
comment: Previous definition "p has_input c if and only c participates_in p at the start of p and c is in some way bound, transported, modified, consumed or destroyed by p." If it is known whether the entity is directly or indirectly bound/acted upon by the gene product that is the subject of the annotation, then the relations has_direct_input or has_indirect_input should be alternatively considered.

Axiom
annotated source: has input
annotated property: has_exact_synonym
annotated target: has_target
database_cross_reference: GOC:ecd

Axiom
annotated source: has input
annotated property: has_narrow_synonym
annotated target: localizes
database_cross_reference: GOC:ecd

has output
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: has participant
inverse of: output of
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
local domain: BFO:0000015
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697
usage: Identifies an entity that is changed or created after participation in a molecular function or biological process
database_cross_reference: RO:0002234
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE chemical
in_subset: AE sequence or complex
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: has_output
comment: Previous definition "p has_output c if c participates_in p at the end of p and c is in some way changed by p or created by p." []

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.
database_cross_reference: RO:0002263
in_subset: valid for go gp2term
shorthand: acts_upstream_of

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.
database_cross_reference: RO:0002264
has_related_synonym: affects
in_subset: valid for go gp2term
shorthand: acts_upstream_of_or_within

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).
IAO_0000116: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002295
shorthand: results_in_developmental_progression_of

results in development of
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 FBbt:00007002 FBbt:10000000 EMAPA:0 ZFA:0100000
usage: The relationship linking an entity and its participation in a process that changes it through time from the formation of the entity to the resultant mature state.
has_alternative_id: GOREL:0001009
database_cross_reference: RO:0002296
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_development_of
comment: Example of use: an annotation of gene X to cell development with results_in_development_of CL:0000540 (neuron) means that gene x is involved in a process where a cell that has an identity of a neuron has gone through a progression from its formation to the resulting mature neuron.

results in formation of anatomical entity
type: ObjectProperty
sub property of: go annotation extension relation
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
definition: The relationship linking a entity and its participation in a process whereby at the beginning of the process the entity does not exist and at the end of the process the entity exists.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
local domain: GO:0008150
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 FBbt:00007002 FBbt:10000000 EMAPA:0 ZFA:0100000
usage: The relationship linking a entity and its participation in a process whereby at the beginning of the process the entity does not exist and at the end of the process the entity exists.
has_alternative_id: GOREL:0001020
database_cross_reference: RO:0002297
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_formation_of
comment: Example of use: 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.

Axiom
annotated source: results in formation of anatomical entity
annotated property: definition
annotated target: The relationship linking a entity and its participation in a process whereby at the beginning of the process the entity does not exist and at the end of the process the entity exists.
database_cross_reference: GOC:mtg_berkeley_2013

results in morphogenesis of
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 FBbt:00007002 FBbt:10000000 EMAPA:0 ZFA:0100000
usage: 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.
has_alternative_id: GOREL:0001015
database_cross_reference: RO:0002298
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_morphogenesis_of
comment: Example of use: 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.

results in maturation of
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: CL:0000000 GO:0005575 PO:0009012 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 FBbt:00007002 FBbt:10000000 EMAPA:0 ZFA:0100000
usage: 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.
has_alternative_id: GOREL:0001013
database_cross_reference: RO:0002299
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_maturation_of
comment: display for curators
comment: Example of use: 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.

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
database_cross_reference: RO:0002304
in_subset: valid for go annotation extension
in_subset: valid for gocam
shorthand: causally_upstream_of,_positive_effect
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
database_cross_reference: RO:0002305
in_subset: valid for go annotation extension
in_subset: valid for gocam
shorthand: causally_upstream_of,_negative_effect

transports or maintains localization of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: related via localization to
sub property of: results in changes to anatomical or cellular structure
definition: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: regulates localization of
local domain: BFO:0000015
local range: CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697
usage: Use to relate a process or molecular function to a substance that is transported, localized or whose localization is maintained by that process or function. The substance may be a chemical, gene product or cellular component. For the movement via locomotion of cells and anatomical structure please use results_in_movement_of.
database_cross_reference: RO:0002313
has_obo_namespace: go/extensions/gorel
has_related_synonym: regulates location of
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cellular component
in_subset: AE chemical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: transports_or_maintains_localization_of

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901
database_cross_reference: RO:0002314
shorthand: characteristic_of_part_of

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: go annotation extension relation
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
local domain: GO:0030154
local range: CL:0000000 PO:0009002 WBbt:0004017 FBbt:00007002 EMAPA:0
usage: Use this relation to link a cell differentiation process to the cell type that the process results in the differentiation of.
has_alternative_id: GOREL:0001014
database_cross_reference: RO:0002315
has_exact_synonym: results in differentiation of
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_acquisition_of_features_of
comment: Example of use: an annotation of gene X to cell differentiation with results_in_acquisition_of_features_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.

ecologically related to
type: ObjectProperty
definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
database_cross_reference: RO:0002321
in_subset: ro-eco
shorthand: ecologically_related_to

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
database_cross_reference: RO:0002323
shorthand: mereotopologically_related_to

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
database_cross_reference: RO:0002324
shorthand: developmentally_related_to

colocalizes with
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: mereotopologically related to
domain: material entity
range: material entity
IAO_0000112: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
database_cross_reference: RO:0002325
in_subset: valid for go gp2term
shorthand: colocalizes_with

contributes to
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: capable of part of
sub property of: part of structure that is capable of
IAO_0000112: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
IAO_0000112: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
IAO_0000112: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
IAO_0000116: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
database_cross_reference: RO:0002326
in_subset: valid for go gp2term
shorthand: contributes_to

enables
type: ObjectProperty
sub property of: go annotation extension relation
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.
database_cross_reference: RO:0002327
in_subset: valid for go gp2term
shorthand: enables

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
database_cross_reference: RO:0002328
shorthand: functionally_related_to

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
database_cross_reference: RO:0002329
shorthand: part_of_structure_that_is_capable_of

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

genomically related to
type: ObjectProperty
domain: continuant
range: continuant
definition: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
database_cross_reference: RO:0002330
shorthand: genomically_related_to

involved in
type: ObjectProperty
sub property of: go annotation extension relation
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
database_cross_reference: RO:0002331
shorthand: involved_in

regulates levels of
type: ObjectProperty
sub property of: go annotation extension relation
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)
has_alternative_id: GOREL:0000036
database_cross_reference: RO:0002332
has_obo_namespace: go/extensions/gorel
shorthand: regulates_level_of

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
database_cross_reference: RO:0002333
in_subset: valid for gocam
shorthand: enabled_by

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)
database_cross_reference: RO:0002334
in_subset: RO_0002259
shorthand: regulated_by

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002335
in_subset: RO_0002259
shorthand: negatively_regulated_by

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002336
in_subset: RO_0002259
shorthand: positively_regulated_by

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.
database_cross_reference: RO:0002337
shorthand: related_via_localization_to

has target start location
type: ObjectProperty
sub property of: go annotation extension relation
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
local range: GO:0005575 CL:0000000 UBERON:0001062
usage: Use to relate a transport or localization process to the starting location of the cargo.
database_cross_reference: RO:0002338
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: has_target_start_location

has target end location
type: ObjectProperty
sub property of: go annotation extension relation
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
local range: GO:0005575 CL:0000000 UBERON:0001062
usage: Use to relate a transport or localization process to the end location of the transported or localized cargo.
database_cross_reference: RO:0002339
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: AE cellular component
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: has_target_end_location

imports
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: transports
definition: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has_alternative_id: GOREL:0000034
database_cross_reference: RO:0002340
has_obo_namespace: go/extensions/gorel
in_subset: valid for go ontology
shorthand: imports

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
database_cross_reference: RO:0002344
shorthand: results_in_transport_to_from_or_in

exports
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: transports
definition: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has_alternative_id: GOREL:0000035
database_cross_reference: RO:0002345
has_obo_namespace: go/extensions/gorel
in_subset: valid for go ontology
shorthand: exports

results in commitment to
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: CL:0000000 WBbt:0004017 FBbt:00007002
usage: The relationship linking a cell and its participation in a process that results in the transition of a cell such that is can only develop into a single cell type.
has_alternative_id: GOREL:0001017
database_cross_reference: RO:0002348
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_commitment_to
comment: Example of use: 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.

results in determination of
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: CL:0000000 WBbt:0004017 FBbt:00007002
usage: The relationship linking a cell and its participation in a process that results in the transition of a cell such that it can only develop into a single cell type independent of its environment.
has_alternative_id: GOREL:0001018
database_cross_reference: RO:0002349
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_determination_of
comment: Example of use: an annotation of gene X to cell determination with results_in_determination_of CL:0000540 (neuron) means that at the end of the process an unspecified cell will develop into a neuron with no additional input.

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
database_cross_reference: RO:0002352
in_subset: RO_0002259
in_subset: ro-eco
shorthand: input_of

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
database_cross_reference: RO:0002353
in_subset: RO_0002259
in_subset: ro-eco
shorthand: output_of

formed as result of
type: ObjectProperty
sub property of: output of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002354
shorthand: formed_as_result_of

results in specification of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: results in developmental progression of
domain: GO_0008150
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
local domain: GO:0008150
local range: CL:0000000 WBbt:0004017 FBbt:00007002
usage: The relationship linking a cell and its participation in a process that results in the transition of a cell such that is can only develop into a single cell type when left in its environment.
has_alternative_id: GOREL:0001021
database_cross_reference: RO:0002356
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_specification_of
comment: display for curators
comment: Example of use: an annotation of gene X to cell determination with results_in_determination_of CL:0000540 (neuron) means that at the end of the process an unspecified cell will develop into a neuron if left in its environment. If the cell is moved, it may develop into a cell type other than a neuron.

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
database_cross_reference: RO:0002404
shorthand: causally_downstream_of

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
database_cross_reference: RO:0002405
shorthand: immediately_causally_downstream_of

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
database_cross_reference: RO:0002407
shorthand: indirectly_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
database_cross_reference: RO:0002409
shorthand: indirectly_negatively_regulates

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
database_cross_reference: RO:0002410
shorthand: causally_related_to

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: go annotation extension relation
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
local domain: BFO:0000015
local range: GO:0008150 GO:0003674
usage: Process A is causally_upstream of process B if process A occurs first, and process A causes process B to happen. Processes A and B do not overlap.
database_cross_reference: RO:0002411
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: causally_upstream_of

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
database_cross_reference: RO:0002412
shorthand: immediately_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)
database_cross_reference: RO:0002413
shorthand: provides_input_for

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)
database_cross_reference: RO:0002414
shorthand: transitively_provides_input_for

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.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: influences (processual)
database_cross_reference: RO:0002418
has_related_synonym: affects
shorthand: causally_upstream_of_or_within

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
database_cross_reference: RO:0002427
in_subset: RO_0002259
shorthand: causally_downstream_of_or_within

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
database_cross_reference: RO:0002428
shorthand: involved_in_regulation_of

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
database_cross_reference: RO:0002429
shorthand: involved_in_positive_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
database_cross_reference: RO:0002430
shorthand: involved_in_negative_regulation_of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: involved in or reguates
database_cross_reference: RO:0002431
shorthand: involved_in_or_involved_in_regulation_of

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
database_cross_reference: RO:0002432
has_exact_synonym: enables activity in
shorthand: is_active_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.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_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.
database_cross_reference: RO:0002434
has_exact_synonym: in pairwise interaction with
in_subset: ro-eco
shorthand: interacts_with

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
database_cross_reference: RO:0002436
shorthand: molecularly_interacts_with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: material entity
range: material entity
definition: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: interacts with on organism level
database_cross_reference: RO:0002437
in_subset: ro-eco
shorthand: biotically_interacts_with

symbiotically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
type: SymmetricProperty
IAO_0000112: whales symbiotically interact with the barnacles that attach to them
definition: A biotic interaction in which the two organisms live together in more or less intimate association.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
database_cross_reference: RO:0002440
in_subset: ro-eco
shorthand: symbiotically_interacts_with

interacts with via parasite-host interaction
type: ObjectProperty
sub property of: symbiotically interacts with
definition: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: This relation groups a pair of inverse relations, parasite of and parasitized by
database_cross_reference: RO:0002443
in_subset: ro-eco
shorthand: interacts_with_via_parasite-host_interaction

parasite of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: interacts with via parasite-host interaction
sub property of: has host
inverse of: parasitized by
IAO_0000112: Pediculus humanus capitis parasite of human
definition: A parasite-host relationship where an organism benefits at the expense of another.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: parasitizes
database_cross_reference: RO:0002444
has_exact_synonym: direct parasite of
in_subset: taxon extension
in_subset: ro-eco
shorthand: parasite_of

parasitized by
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: host of
definition: Inverse of parasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has parasite
IAO_0000118: parasitised by
database_cross_reference: RO:0002445
has_exact_synonym: directly parasitized by
in_subset: ro-eco
shorthand: parasitized_by

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
database_cross_reference: RO:0002447
shorthand: phosphorylates

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
database_cross_reference: RO:0002448
has_exact_synonym: molecularly controls
shorthand: directly_regulates_activity_of

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
database_cross_reference: RO:0002449
has_exact_synonym: molecularly decreases activity of
shorthand: directly_negatively_regulates_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
database_cross_reference: RO:0002450
has_exact_synonym: molecularly increases activity of
shorthand: directly_positively_regulates_activity_of

host of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: symbiotically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
database_cross_reference: RO:0002453
in_subset: taxon extension
in_subset: ro-eco
shorthand: host_of

has host
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: symbiotically interacts with
definition: X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002454
in_subset: taxon extension
in_subset: ro-eco
shorthand: has_host

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
database_cross_reference: RO:0002479
in_subset: ro-eco
shorthand: has_part_that_occurs_in

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

relation between physical entity and a process or stage
type: ObjectProperty
domain: independent continuant
range: occurrent
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
database_cross_reference: RO:0002487
shorthand: relation_between_physical_entity_and_a_process_or_stage

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
definition: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002488
shorthand: existence_starts_during

existence overlaps
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: relation between physical entity and a process or stage
definition: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
local domain: BFO:0000004
local range: GO:0008150 WBls:0000075 ZFS:0100000 FBdv:00007012
usage: Identifies a process or life stage during which a cellular component is present
database_cross_reference: RO:0002490
in_subset: AE biological process
in_subset: AE developmental stages
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: existence_overlaps
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts and ends during
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: existence starts during
sub property of: existence ends during
definition: x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
local domain: BFO:0000004
local range: GO:0008150 WBls:0000075 ZFS:0100000 FBdv:00007012
usage: Identifies a process or life stage during which a cellular component is present
database_cross_reference: RO:0002491
has_exact_synonym: exists during
in_subset: AE biological process
in_subset: AE developmental stages
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: existence_starts_and_ends_during
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
definition: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002492
shorthand: existence_ends_during
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: preceded by
definition: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002496
shorthand: existence_starts_during_or_after
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: precedes
definition: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002497
shorthand: existence_ends_during_or_before
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations
database_cross_reference: RO:0002500
shorthand: causal_agent_in_process

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.
database_cross_reference: RO:0002501
shorthand: causal_relation_between_processes

depends on
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002502
shorthand: depends_on

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
database_cross_reference: RO:0002506
shorthand: causal_relation_between_entities

hyperparasite of
type: ObjectProperty
sub property of: has host
inverse of: hyperparasitized by
property chain axiom: parasite of
definition: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000116: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
database_cross_reference: RO:0002553
has_narrow_synonym: hyperparasitoid of
has_related_synonym: epiparasite of
in_subset: ro-eco
shorthand: hyperparasite_of

hyperparasitized by
type: ObjectProperty
sub property of: host of
property chain axiom: parasitized by
definition: inverse of hyperparasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002554
has_related_synonym: has epiparasite
has_related_synonym: has hyperparasite
has_related_synonym: hyperparasitoidized by
in_subset: RO_0002259
in_subset: ro-eco
shorthand: hyperparasitized_by

pathogen of
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: has host
inverse of: has pathogen
definition: Inverse of has pathogen
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002556
in_subset: taxon extension
in_subset: ro-eco
shorthand: pathogen_of

has pathogen
type: ObjectProperty
sub property of: go annotation extension relation
sub property of: host of
definition: A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002557
in_subset: taxon extension
in_subset: ro-eco
shorthand: has_pathogen

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)
database_cross_reference: RO:0002559
shorthand: causally_influenced_by

results in movement of
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: GO:0008150
local range: CL:0000000 WBbt:0004017 FBbt:00007002 EMAPA:0
usage: Use this relation to link a locomotion process to the type of cell or anatomical structure or organism that the process results in locomotion of.
has_alternative_id: GOREL:0001001
database_cross_reference: RO:0002565
has_obo_namespace: go/extensions/gorel
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: results_in_movement_of
comment: For movement of chemicals or cell parts, please use transports_or_maintains_localization_of

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)
database_cross_reference: RO:0002566
shorthand: causally_influences

participates in a biotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
domain: organism
range: organism
IAO_0000117: https://orcid.org/0000-0002-6601-2165
database_cross_reference: RO:0002574
in_subset: ro-eco
shorthand: participates_in_a_biotic-biotic_interaction_with

directly regulates
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: BFO:0000015
database_cross_reference: RO:0002578
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: directly_regulates

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
database_cross_reference: RO:0002584
shorthand: has_part_structure_that_is_capable_of

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
database_cross_reference: RO:0002595
shorthand: causal_relation_between_material_entity_and_a_process

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
database_cross_reference: RO:0002596
shorthand: capable_of_regulating

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
database_cross_reference: RO:0002597
shorthand: capable_of_negatively_regulating

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
database_cross_reference: RO:0002598
shorthand: capable_of_positively_regulating

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations
database_cross_reference: RO:0002608
shorthand: process_has_causal_agent

directly positively regulates
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: BFO:0000015
database_cross_reference: RO:0002629
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: directly_positively_regulates

directly negatively regulates
type: ObjectProperty
sub property of: go annotation extension relation
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
local domain: BFO:0000015
local range: BFO:0000015
database_cross_reference: RO:0002630
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: AE biological process
in_subset: AE molecular function
in_subset: display for curators
in_subset: valid for annotation extension
shorthand: directly_negatively_regulates

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
database_cross_reference: RO:0003000
in_subset: ro-eco
shorthand: produces
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
local domain: GO:0005575
local range: CL:0000000
usage: Use this relation to link a cell component that is the product of a cell, to the cell-type that produced it. Examples include recording the cell type that produces an exosome, an LDL, or a secreted ECM component.
database_cross_reference: RO:0003001
in_subset: AE cell or anatomical
in_subset: display for curators
in_subset: valid for annotation extension
in_subset: ro-eco
shorthand: produced_by

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
database_cross_reference: RO:0004031
shorthand: enables_subfunction

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
database_cross_reference: RO:0004032
in_subset: valid for go gp2term
shorthand: acts_upstream_of_or_within,_positive_effect

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
database_cross_reference: RO:0004033
in_subset: valid for go gp2term
shorthand: acts_upstream_of_or_within,_negative_effect

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
database_cross_reference: RO:0004034
in_subset: valid for go gp2term
shorthand: acts_upstream_of,_positive_effect

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
database_cross_reference: RO:0004035
in_subset: valid for go gp2term
shorthand: acts_upstream_of,_negative_effect

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
database_cross_reference: RO:0004046
shorthand: causally_upstream_of_or_within,_negative_effect

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
database_cross_reference: RO:0004047
shorthand: causally_upstream_of_or_within,_positive_effect

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
database_cross_reference: RO:0011002
shorthand: regulates_activity_of

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
database_cross_reference: RO:0012011
shorthand: indirectly_causally_upstream_of

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
database_cross_reference: RO:0012012
shorthand: indirectly_regulates

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
database_cross_reference: RO:0017001
shorthand: device_utilizes_material

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
database_cross_reference: RO:0019000
shorthand: regulates_characteristic

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
database_cross_reference: RO:0019001
shorthand: positively_regulates_characteristic

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
database_cross_reference: RO:0019002
shorthand: negatively_regulates_characteristic

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
database_cross_reference: RO:0020105
shorthand: is_anatomical_entity

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
database_cross_reference: RO:0040036
shorthand: results_in_changes_to_anatomical_or_cellular_structure

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
disjoint with: generically dependent continuant
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

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
disjoint with: generically dependent continuant
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.

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

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: generically dependent continuant
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
IAO_0000116: Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

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.
IAO_0000116: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
IAO_0000116: 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

organism
type: Class
subclass of: material anatomical entity
definition: A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome
IAO_0000116: 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.
IAO_0000116: Includes virus - we will later have a class for cellular organisms.

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.
IAO_0000116: 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

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

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon 4751
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FAO:0000001
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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon 4751
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
id: UBERON:0000465
in_subset: common anatomy
in_subset: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon 4751
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BFO:0000004
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
id: UBERON:0001062
in_subset: common anatomy
in_subset: 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

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

BFO_0000060
definition: OBSOLETE. Was not defined before obsoletion.

RO_0002401
definition: OBSOLETE. Was not defined before obsoletion.

RO_0002403
definition: OBSOLETE. Was not defined before obsoletion.

RO_0002406
in_subset: AE molecular function
local range: GO:0003674
local domain: GO:0003674

RO_0002408
in_subset: AE molecular function
local domain: GO:0003674
local range: GO:0003674

RO_0004008
in_subset: valid for go ontology
in_subset: AE molecular function
in_subset: valid for gocam
in_subset: display for curators
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697
in_subset: valid for annotation extension
in_subset: valid for go annotation extension
in_subset: AE biological process
local domain: BFO:0000015

RO_0004009
in_subset: valid for go ontology
in_subset: display for curators
in_subset: AE molecular function
in_subset: valid for annotation extension
local range: CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697 SO:0000839 SO:0001683 NCBITaxon:1
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: AE biological process
local domain: BFO:0000015

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