format-version: 1.2
default-namespace: go/extensions/gorel
ontology: go_annotation_relations
remark: A collection of relations that can be used in GO annotation to create anonymous classes via col16.
remark: Many of these relations are independently defined elsewhere, or will eventually be independently defined elsewhere.
remark: The purpose of this ontology is to MIREOT these relations together, in one place.
remark: Some of these relations may also have declarations in the main GO file.
remark: They will have additional axioms attached here, such as domain and range constraints, that for technical reasons we do not yet put in the main GO file.
remark: Notes:
remark: When interpreting domain/range constraints, remember that MF isa bfo:Process
remark: OBO-Format reminder:
remark: holds_over_chain is used to define "triad" rules; e.g. R holds_over_chain R1 R2 means: if x R1 y and y R2 z then x R z.
remark: is_transitive is the same as R holds_over_chain R R.
remark: in a relationship x R y, x must be a subtype of the domain and y must be a subtype of the range
remark: GOREL ID ranges: CJM 1-500; PomBase/MAH 501-750
remark: go_annotation_extension_relations.obo made consistent with contents of this file 2012-04-19

[Typedef]
id: part_of
name: part_of
xref: BFO:0000050
is_transitive: true
inverse_of: has_part

[Typedef]
id: has_part
name: has_part
is_transitive: true
xref: BFO:0000051

[Typedef]
id: occurs_in
name: occurs_in
def: "p occurs_in c if and only if all of the participants of p are part_of c." [BFO:cjm]
xref: BFO:0000066
domain: BFO:0000007 ! process
range: BFO:0000004 ! independent continuant
holds_over_chain: part_of occurs_in
holds_over_chain: occurs_in part_of

[Typedef]
id: happens_during
name: happens_during
def: "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]
comment: Note that in order to express that part_of between processes implies during, we must use OWL.
is_transitive: true
domain: BFO:0000007 ! process
range: BFO:0000007 ! process
xref: GOREL:0000001

[Typedef]
id: exists_during
name: exists_during
def: "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]
is_transitive: false
domain: BFO:0000004 ! independent continuant
range: BFO:0000007 ! process
xref: GOREL:0000001

[Typedef]
id: during
name: during
def: "happens_during or exists_during." [BFO:cjm]
is_transitive: true
domain: BFO:0000001 ! entity
range: BFO:0000007 ! process
union_of: happens_during
union_of: exists_during
xref: GOREL:0000002

[Typedef]
id: localizes_to
name: localizes_to
synonym: "localization_destination" EXACT [GOC:mah]
comment: TODO : check this one. Note Pombe is using different variant.
def: "c localizes_to d if c executes some function when it is part_of d." [BFO:cjm]
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
holds_over_chain: localizes_to part_of
xref: GOREL:0000003

[Typedef]
id: dependent_on
name: dependent_on
def: "." [BFO:cjm]
comment: TODO - Pombe uses 4 variants for <process,physical entity> x <process,physical entity>. Document each one.
domain: BFO:0000001 ! entity
range: BFO:0000001 ! entity
xref: GOREL:0000004

![Typedef]
!id: located_at
!name: located_at
!comment: TODO. Pombe uses this with both BP and CC as range. How does this differ from occurs_in / part_of? Perhaps it means "in vicinity of"??
!domain: BFO:0000001 ! entity
!range: BFO:0000004 ! independent continuant
!holds_over_chain: localizes_to part_of
! S. pombe will change these to occurs_in
!xref: GOREL:0000005

[Typedef]
id: has_target_cell
name: has_target_cell
comment: this is a very generic relation and it's direct use is discouraged for curation. It exists to retrofit legacy annotations.
domain: BFO:0000001 ! entity
range: CL:0000000 ! cell
xref: GOREL:0000006
! not sure whether this should be related to newer has_target, or, if so, how; would require has_target domain & range changes

[Typedef]
id: has_target_anatomical_entity
name: has_target_anatomical_entity
comment: this is a very generic relation and it's direct use is discouraged for curation. It exists to retrofit legacy annotations.
domain: BFO:0000001 ! entity
range: CARO:0000000 ! anatomical entity
xref: GOREL:0000007
! not sure whether this should be related to newer has_target, or, if so, how; would require has_target domain & range changes

[Typedef]
id: has_participant
name: has_participant
xref: BFO:0000057

[Typedef]
id: OBO_REL:has_input
name: has_input
def: "Instance-level: p has_input c iff c participates_in p at t0 (where t0 is the start of p) and c is in some way changed by p. Type-level: P has_input C iff all instances p of P has_input some C" []
is_a: OBO_REL:has_participant
! copied from relations_process_xp.obo file; added is_a link

[Typedef]
id: OBO_REL:has_output
name: has_output
def: "Instance-level: p has_output c iff c participates_in p at t' (where t' is the end of p) and c is in some way changed by p. Type-level: P has_output C iff all instances p of P has_output some C" []
is_a: OBO_REL:has_participant
! copied from relations_process_xp.obo file, added is_a link

[Typedef]
id: localization_dependent_on
name: localization_dependent_on
def: "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]
domain: GO:0005575 ! cellular_component
!range: union_of (BFO:0000004 ! independent continuant and GO:0008150 ! biological_process)
is_a: dependent_on
! not sure how to write out the range specification ... or text def, for that matter
! could consider subtypes for
!  localization_dependent_on_gene_product (range: gene products)
!  localization_dependent_on_CC (range: GO CC)
!  localization_dependent_on_BP (range: GO BP)
!  localization_dependent_on_protein_feature (range: protein features, including domains)
! 2012-02-01 annotation extension meeting: also want to include GO MFs in range
xref: GOREL:0000009

[Typedef]
id: requires_sequence_feature
name: requires_sequence_feature
def: "OBSOLETE. A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in MF or BP." [GOC:mah]
comment: obsolete because strictly speaking, these fall outside the scope of GO, even with extended annotations; only used for a few PomBase annotations, which will be changed accordingly
synonym: "requires_feature" BROAD [GOC:mah]
domain: BFO:0000007 ! process
!range: protein features, e.g. Pfam domains, InterPro signatures
! TODO: ask ColinB for the relevant SOM class to use as the range
! also extend range to nucleic acid features, for annotations of functional RNAs?
! alternate name - via_feature?
! broad synonym used to be the ID and name; both made more specific for clarity
is_obsolete: true
xref: GOREL:0000010

[Typedef]
id: requires_direct_regulator
name: requires_regulator
def: "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." [GOC:mah]
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)
domain: GO:0003674 ! molecular_function
range: TEMP:0000001 ! gene product or complex
is_a: requires_regulator ! requires_regulator
! is there a way to formally specify the restriction described in the comment?
xref: GOREL:0000502

[Typedef]
id: requires_regulator
name: requires_regulator
def: "annotated gene product requires regulation by the gene product or complex for its participation in MF or BP" [GOC:mah]
domain: BFO:0000007 ! process
range: TEMP:0000001 ! gene product or complex
is_a: dependent_on
! is there a way to formally specify the restriction described in the comment?
xref: GOREL:0000011

[Typedef]
id: requires_substance
name: requires_substance
def: "annotated gene product participates in BP or executes MF only in presence of substance" [GOC:mah]
domain: BFO:0000007 ! process
range: CHEBI:24331 ! chemical entity
is_a: dependent_on
! domain: GO:0008150 ! biological_process + GO:0003674 ! molecular_function
! really not sure of name for this one; also considering "dependent_on_substance" and "dependent_on_molecule", and don't really like any of them
! questions: extend domain to MF? extend range to gene product? lump with requires_regulator?
xref: GOREL:0000012

[Typedef]
id: independent_of
name: independent_of
def: "localization to CC occurs whether BP occurs or not" [GOC:mah]
comment: The pre-composed CC is kind of odd here. On the one hand we want to talk about the process of localization here, but we might want to remain silent on what gene product is involved in this localization.
domain: GO:0005575 ! cellular_component
range: GO:0008150 ! biological_process
xref: GOREL:0000013

[Typedef]
id: inhibits_protease
name: inhibits_protease
def: "OBSOLETE. Identifies a specific target of regulation of a MF" [GOC:mah]
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.
domain: GO:0010466 ! negative regulation of peptidase activity
range: TEMP:0000002 ! gene product
is_obsolete: true
xref: GOREL:0000014

[Typedef]
id: protease_activator
name: protease_activator
def: "OBSOLETE. Identifies a specific target of regulation of a MF" [GOC:mah]
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.
domain: GO:0010952 ! positive regulation of peptidase activity
range: TEMP:0000002 ! gene product
is_obsolete: true
xref: GOREL:0000017

[Typedef]
id: stabilizes
name: stabilizes
def: "Identifies specific gp stabilized in a protein stabilization process (or regulation thereof)" [GOC:mah]
domain: GO:0050821 ! protein stabilization
range: TEMP:0000001 ! gene product or complex
is_a: OBO_REL:has_participant
! this is almost absurdly specific; lump into something broader, e.g. has_substrate? has_input?
xref: GOREL:0000018

[Term]
id: TEMP:0000001
name: gene product or complex
comment: define as union of RNA product (SOM), PR:000000001 ! protein, GO:0032991 ! macromolecular complex

[Term]
id: TEMP:0000002
name: gene product
comment: define as union of RNA product (SOM), PR:000000001 ! protein

[Term]
id: TEMP:0000003
name: gene or gene product
comment: define as union of SO:0000704 ! gene, RNA product (SOM), PR:000000001 ! protein

[Term]
id: TEMP:0000004
name: catalytic activity or transporter activity
comment: define as union of GO:0003824 catalytic activity + GO:0005215 ! transporter activity

[Term]
id: TEMP:0000005
name: chemical, gene product, or complex
comment: define as union of RNA product (SOM), PR:000000001 ! protein, GO:0032991 ! macromolecular complex, and CHEBI:23367 ! molecular entity

[Typedef]
id: transcriptionally_regulates
name: transcriptionally_regulates
def: "OBSOLETE. Identifies gene whose transcription is regulated" [GOC:mah]
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.
domain: GO:0006355 ! regulation of transcription, DNA-dependent
! range: gene
is_obsolete: true
xref: GOREL:0000023

[Typedef]
id: not_during
name: not_during
def: "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)." [GOC:mah]
comment: domain can be any process or object or even quality
domain: BFO:0000001 ! entity
range: BFO:0000007 ! process
is_class_level: true
! placeholder that will probably be superseded by something more clever later
xref: GOREL:0000024

[Typedef]
id: not_happens_during
name: not_happens_during
def: "A BP during which an annotation to a BP does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases)." [GOC:mah]
synonym: "does_not_happen_during" EXACT [GOC:mah]
domain: BFO:0000007 ! process
range: BFO:0000007 ! process
is_a: not_during
is_class_level: true
! placeholder that will probably be superseded by something more clever later
xref: GOREL:0000025

[Typedef]
id: not_exists_during
name: not_exists_during
def: "A BP during which an annotation to a CC does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases)." [GOC:mah]
synonym: "does_not_exist_during" EXACT [GOC:mah]
domain: BFO:0000004 ! independent continuant
range: BFO:0000007 ! process
is_a: not_during
is_class_level: true
! placeholder that will probably be superseded by something more clever later
xref: GOREL:0000026

[Typedef]
id: in_presence_of
name: in_presence_of
def: "Identifies a continuant in the presence of which an ontology term is observed to apply to the annotated gene product." [GOC:mah]
range: BFO:0000004 ! independent continuant
! domain: includes GO, and maybe also others
! some of the children of dependent_on may also be is_a children of this relation
xref: GOREL:0000027

[Typedef]
id: requires_localization
name: requires_localization
def: "annotated gene product participates in BP only if BP is located at CC" [GOC:mah]
synonym: "dependent_on_localization" EXACT [GOC:mah]
domain: GO:0008150 ! biological_process
range: GO:0005575 ! cellular_component
is_a: dependent_on
xref: GOREL:0000028

[Typedef]
id: requires_regulation_by
name: requires_regulation_by
def: "annotated gene product participates in BP or executes MF activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)" [GOC:mah]
domain: BFO:0000007 ! process
range: TEMP:0000001 ! gene product or complex
xref: GOREL:0000029

[Typedef]
id: modified_by
name: modified_by
def: "Identifies the gene product that catalyzes a modification on the annotated gene product" [GOC:mah]
domain: MOD:00000 ! protein modification
range: TEMP:0000001 ! gene product or complex
! We're using this  in pombase to extend protein modification annotations using PSI-MOD. Apologies for shamelessly stuffing this into the GO col16 relations collection; we don't have a better place for it at the moment --mah, vw, al
xref: GOREL:0000030

[Typedef]
id: condition
name: condition
def: "OBSOLETE. Identifies a condition under which the ontology term is observed to apply to the annotated gene product" [GOC:mah]
comment: obsolete because not actually used for GO annotation extensions; shoehorned in here in the first place
synonym: "under_condition" EXACT [GOC:mah]
synonym: "assay_condition" EXACT [GOC:mah]
! domain: includes GO and FYPO, and maybe also others
! another pombase extension shoehorned here for the time being ... range is from a manually "controlled" vocabulary at the moment
is_obsolete: true
xref: GOREL:0000031

[Typedef]
id: occurs_at
name: occurs_at
def: "P occurs_at C : the execution of P is located at C." [GOC:cjm, GOC:mah]
comment: 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.
xref: GOREL:0000501

[Typedef]
id: requires_modification
name: requires_modification
def: "Annotated gene product must be modified as described by extension to participate in MF or BP." [GOC:mah]
comment: obsolete because can use PR or SOM ID in column 17 instead
domain: BFO:00000007 ! process
range: MOD:00000 ! protein modification
! is range ok? or will we also want to allow for modified functional RNAs?
is_obsolete: true
xref: GOREL:0000502

[Typedef]
id: has_target
name: has_target
def: "Identifies an entity affected by the gene product's participation in MF or BP." [GOC:mah]
domain: BFO:00000007 ! process
range: TEMP:0000005 ! chemical, gene product, or complex
is_a: has_participant ! has_participant
xref: GOREL:0000503

[Typedef]
id: has_direct_target
name: has_direct_target
def: "Identifies an entity directly affected by a gene product's activity (execution of MF)." [GOC:mah]
domain: GO:0003674 ! molecular_function
range: TEMP:0000005 ! chemical, gene product, or complex
is_a: has_target ! has_target
xref: GOREL:0000504
! would be more correct to say the activity is the target range, but we have to use molecules or complexes as proxies for their activities at present

[Typedef]
id: has_substrate
name: has_substrate
def: "Identifies the gene product on which a catalytic MF acts" [GOC:mah]
comment: could merge this into has_direct_target, because annotating to a descendant of GO:0003824 captures the specificity anyway (child relation is redundant)
domain: GO:0003824 ! catalytic_activity
range: TEMP:0000005 ! chemical, gene product, or complex
is_a: OBO_REL:has_input ! Q: keep this relation?
is_a: has_direct_target ! has_direct_target
xref: GOREL:0000019

[Typedef]
id: has_indirect_target
name: has_indirect_target
def: "Identifies a gene or gene product affected by a regulation BP." [GOC:mah]
synonym: "has_regulation_target" RELATED [GOC:curators]
domain: GO:0065007 ! biological regulation
range: TEMP:0000003 ! gene or gene product
is_a: has_target ! has_target
xref: GOREL:0000015

[Typedef]
id: localizes
name: localizes
def: "Identifies the gene product or substance whose location is established or maintained by a localization process." [GOC:mah]
synonym: "localization_target_is" RELATED [GOC:mah]
domain: GO:0051179 ! localization
range: TEMP:0000001 ! gene product or complex
is_a: has_target ! has_target
! we may decide to pre-compose all terms that would otherwise use this relation for range: GO CC, but do we also want to pre-compose for range: gene product?
xref: GOREL:0000016

[Typedef]
id: has_upstream_or_downstream_target
name: has_upstream_or_downstream_target
domain: GO:0008150 ! biological_process
range: TEMP:0000001 ! gene product or complex
xref: GOREL:0000020
is_obsolete: true
comment: obsolete because it's hardly been used and 2012-02-01 meeting participants couldn't tell how to define or use it
! 2012-02-10 see note on has_upstream_target

[Typedef]
id: has_upstream_target
name: has_upstream_target
domain: GO:0008150 ! biological_process
range: TEMP:0000001 ! gene product or complex
xref: GOREL:0000021
is_obsolete: true
comment: obsolete because it's never been used and 2012-02-01 meeting participants couldn't tell how to define or use it
! as of 2012-02-01, not used and meeting participants don't know what this should mean nor how it should be used. use cases welcome.

[Typedef]
id: has_downstream_target
name: has_downstream_target
domain: GO:0008150 ! biological_process
range: TEMP:0000001 ! gene product or complex
xref: GOREL:0000022
is_obsolete: true
comment: obsolete because it's seldom used and 2012-02-01 meeting participants couldn't tell how to define or use it
! 2012-02-01 meeting: much discussion of this, as we realized that we haven't agreed on how it should be defined and used. considering possibility of merging with has_regulation_target, but need to see more examples before final decision
!  another possibility: has_regulation_target is_a has_downstream_target
!  also consider has_substrate is_a has_downstream_target ... or some other way to link them?
!  and a new relation that's is_a has_substrate AND has_regulation_target ???
!    but remember the bit about has_substrate being direct ... and whether has_regulation_target needs children for direct and indirect
! or just get rid of this, and add use regulates???

[Typedef]
id: directly_localizes
name: directly_localizes
def: "Identifies the gene product or substance whose location is established or maintained by the direct action of the annotated gene product." [GOC:mah]
domain: GO:0051179 ! localization
range: TEMP:0000001 ! gene product or complex
is_a: localizes
is_a: has_direct_target
xref: GOREL:0000504
! may merge into has_direct_target (narrow synonym)

[Typedef]
id: indirectly_localizes
name: indirectly_localizes
def: "Identifies the gene product or substance whose location is established or maintained a process in which the annotated gene product is involved, but where the annotated gene product is known not to act directly." [GOC:mah]
domain: GO:0051179 ! localization
range: TEMP:0000001 ! gene product or complex
is_a: localizes
is_a: has_indirect_target
xref: GOREL:0000505
! may merge into has_indirect_target (narrow synonym)

[Typedef]
id: not_occurs_in
name: not_occurs_in
def: "An entity (e.g. cell type or CC) in which a BP or MF does not occur. Opposite of occurs_in." [GOC:mah]
xref: GOREL:0000506
domain: BFO:0000007 ! process
range: BFO:0000004 ! independent continuant