format-version: 1.2
subsetdef: AE_biological_process "GO biological process"
subsetdef: AE_cell_or_anatomical "cell or anatomical"
subsetdef: AE_cellular_component "GO cellular component"
subsetdef: AE_chemical "Chemical"
subsetdef: AE_developmental_stages "Developmental stages"
subsetdef: AE_molecular_function "GO molecular function"
subsetdef: AE_sequence_feature "Sequence feature"
subsetdef: AE_sequence_or_complex "Protein, protein complex, gene or transcript identifier"
subsetdef: display_for_curators ""
subsetdef: taxon_extension ""
subsetdef: valid_for_annotation_extension ""
synonymtypedef: RO:0008000 "display label for users"
default-namespace: external
remark: Includes Ontology(OntologyID(Anonymous-3)) [Axioms: 1172 Logical Axioms: 303]
ontology: go/extensions/gorel
property_value: http://purl.org/dc/elements/1.1/description "This ontology combines RO together with GO-specific relations in the GOREL namespace, used for annotation extensions. See;\n\nHuntley, 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\n\nNotes on release edition (gorel.owl):\n\nThis ontology is created by merging the relevant subset of RO together with GO-specific annotations of RO relations, and GOREL relations\n\nNotes on editors version (gorel-edit.owl): \nThe 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" xsd:string
[Typedef]
id: activated_by
name: activated_by
namespace: go/extensions/gorel
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.
subset: AE_chemical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "activated by" EXACT RO:0008000 [PomBase:curators]
synonym: "activated_by_chemical" EXACT [GOC:mah]
synonym: "activated_by_substance" EXACT [GOC:mah]
synonym: "activity_increased_by" EXACT [GOC:mah]
xref: GOREL:0000507
property_value: local_domain GO:0003674 xsd:string
property_value: local_range CHEBI:24431 xsd:string
property_value: usage "Identifies a chemical substance that increases the activity of the gene product." xsd:string
domain: GO:0003674
range: CHEBI:24431
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: actively_participates_in
name: actively participates in
def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
xref: RO:0002217
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "agent in" xsd:string
is_a: participates_in ! participates in
inverse_of: has_agent ! has active participant
[Typedef]
id: acts_on_population_of
name: acts_on_population_of
namespace: go/extensions/gorel
def: "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." [GOC:mtg_berkeley_2013]
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001006
property_value: local_domain GO:0008283 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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.)" xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
[Typedef]
id: acts_upstream_of
name: acts upstream of
def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" []
xref: RO:0002263
holds_over_chain: enables causally_upstream_of
is_a: acts_upstream_of_or_within ! acts upstream of or within
[Typedef]
id: acts_upstream_of_or_within
name: acts upstream of or within
def: "c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p" []
synonym: "affects" RELATED []
xref: RO:0002264
holds_over_chain: enables causally_upstream_of_or_within
is_a: causal_agent_in ! causal agent in
[Typedef]
id: adjacent_to
name: adjacent to
namespace: go/extensions/gorel
def: "x adjacent to y if and only if x and y share a boundary." []
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "adjacent to" EXACT RO:0002220 []
xref: RO:0002220
property_value: 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." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"}
property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string
property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: local_domain GO:0005575 xsd:string
property_value: local_range "GO:0005575 CL:0000000" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000004
range: BFO:0000004
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: spatially_disjoint_from ! spatially disjoint from
[Typedef]
id: axis_of
name: axis_of
namespace: go/extensions/gorel
xref: GOREL:0001000
[Typedef]
id: bearer_of
name: bearer of
def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" []
xref: RO:0000053
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: 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." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
range: BFO:0000020
[Typedef]
id: biotically_interacts_with
name: biotically interacts with
def: "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." []
subset: ro-eco
xref: RO:0002437
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "interacts with on organism level" xsd:string
property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005
property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string
domain: BFO:0000040
range: BFO:0000040
is_symmetric: true
is_a: ecologically_related_to ! ecologically related to
is_a: interacts_with ! interacts with
[Typedef]
id: capable_of
name: capable of
def: "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. " []
subset: ro-eco
xref: RO:0002215
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: 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)\"." xsd:string
domain: BFO:0000004
range: BFO:0000015
is_a: capable_of_part_of ! capable of part of
expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" []
[Typedef]
id: capable_of_negatively_regulating
name: capable of negatively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." []
xref: RO:0002597
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: capable_of negatively_regulates
is_a: capable_of_regulating ! capable of regulating
[Typedef]
id: capable_of_part_of
name: capable of part of
def: "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." []
xref: RO:0002216
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: causal_agent_in ! causal agent in
is_a: functionally_related_to ! functionally related to
expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" []
[Typedef]
id: capable_of_positively_regulating
name: capable of positively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." []
xref: RO:0002598
property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: capable_of positively_regulates
is_a: capable_of_regulating ! capable of regulating
[Typedef]
id: capable_of_regulating
name: capable of regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." []
xref: RO:0002596
property_value: IAO:0000112 "pyrethroid -> growth" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: capable_of regulates
is_a: causal_agent_in ! causal agent in
[Typedef]
id: causal_agent_in
name: causal agent in
def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" []
xref: RO:0002500
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process
inverse_of: has_causal_agent ! has causal agent
[Typedef]
id: causal_relation_between_material_entities
name: causal relation between material entities
xref: RO:0002506
property_value: 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" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: 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." xsd:string
domain: BFO:0000040
range: BFO:0000040
is_a: causally_related_to ! causally related to
[Typedef]
id: causal_relation_between_material_entity_and_a_process
name: causal relation between material entity and a process
def: "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." []
xref: RO:0002595
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
domain: BFO:0000040
range: BFO:0000015
is_a: causally_related_to ! causally related to
[Typedef]
id: causal_relation_between_processes
name: causal relation between processes
def: "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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." []
xref: RO:0002501
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: 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." xsd:string
domain: BFO:0000003
range: BFO:0000003
is_a: causally_related_to ! causally related to
[Typedef]
id: causally_downstream_of
name: causally downstream of
def: "inverse of upstream of" []
xref: RO:0002404
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: causally_downstream_of_or_within ! causally downstream of or within
is_a: preceded_by ! preceded by
inverse_of: causally_upstream_of ! causally upstream of
[Typedef]
id: causally_downstream_of_or_within
name: causally downstream of or within
def: "inverse of causally upstream of or within" []
subset: RO:0002259
xref: RO:0002427
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_transitive: true
is_a: causal_relation_between_processes ! causal relation between processes
[Typedef]
id: causally_influenced_by
name: causally influenced by
xref: RO:0002559
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string
is_a: causal_relation_between_material_entities ! causal relation between material entities
inverse_of: causally_influences ! causally influences
[Typedef]
id: causally_influences
name: causally influences
def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" []
xref: RO:0002566
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string
is_a: causal_relation_between_material_entities ! causal relation between material entities
[Typedef]
id: causally_related_to
name: causally related to
def: "This relation groups causal relations between material entities and causal relations between processes" []
xref: RO:0002410
property_value: IAO:0000114 IAO:0000428
property_value: 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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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." xsd:string
is_a: related_via_dependence_to ! related via dependence to
[Typedef]
id: causally_upstream_of
name: causally upstream of
namespace: go/extensions/gorel
def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002411
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "GO:0008150 GO:0003674" xsd:string
property_value: 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." xsd:string
is_transitive: true
is_a: causally_upstream_of_or_within ! causally upstream of or within
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: precedes ! precedes
[Typedef]
id: causally_upstream_of,_negative_effect
name: causally upstream of, negative effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
xref: RO:0002305
property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string
is_a: causally_upstream_of ! causally upstream of
[Typedef]
id: causally_upstream_of,_positive_effect
name: 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
xref: RO:0002304
property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string
is_a: causally_upstream_of ! causally upstream of
[Typedef]
id: causally_upstream_of_or_within
name: causally upstream of or within
def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." []
synonym: "affects" RELATED []
xref: RO:0002418
property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "influences (processual)" xsd:string
is_transitive: true
is_a: causal_relation_between_processes ! causal relation between processes
inverse_of: causally_downstream_of_or_within ! causally downstream of or within
[Typedef]
id: coincident_with
name: coincident with
def: "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." []
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.
subset: AE_cellular_component
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0002008
property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: local_domain GO:0005575 xsd:string
property_value: local_range "CHEBI:24431 SO:0000001 SO:0000704" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: mereotopologically_related_to ! mereotopologically related to
[Typedef]
id: colocalizes_with
name: colocalizes with
def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." []
xref: RO:0002325
property_value: http://purl.org/dc/elements/1.1/creator "Gene Ontology Consortium" xsd:string
property_value: 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)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with xsd:string
property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string
domain: BFO:0000040
range: BFO:0000040
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: mereotopologically_related_to ! mereotopologically related to
[Typedef]
id: condition
name: condition
namespace: go/extensions/gorel
def: "Identifies a condition under which the ontology term is observed to apply to the annotated gene product" [GOC:mah]
synonym: "assay_condition" EXACT [GOC:mah]
synonym: "under_condition" EXACT [GOC:mah]
xref: GOREL:0000031
property_value: usage "Identifies a condition under which the ontology term is observed to apply to the annotated gene product" xsd:string
is_obsolete: true
[Typedef]
id: contains_process
name: contains process
def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
xref: BFO:0000067
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Typedef]
id: contributes_to
name: contributes to
xref: RO:0002326
property_value: 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." xsd:string
property_value: 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" xsd:string
property_value: 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." xsd:string
property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to xsd:string
property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string
is_a: capable_of_part_of ! capable of part of
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of
[Typedef]
id: dependent_on
name: dependent_on
namespace: go/extensions/gorel
def: "Identifies a requirement under which the ontology term is observed to apply to the annotated gene product." [GOC:rph]
comment: PomBase uses the more specific child relations, and avoids using dependent_on directly.
subset: AE_biological_process
subset: AE_chemical
subset: AE_molecular_function
subset: AE_sequence_feature
subset: AE_sequence_or_complex
subset: valid_for_annotation_extension
synonym: "dependent on" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000004
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "CHEBI:24431 GO:0003674 GO:0008150 GO:0032991 MI:0315 MOD:00000 PR:000000001 SO:0000110 SO:0000673 SO:0000704 CHEBI:33697" xsd:string
property_value: usage "Identifies a requirement under which the ontology term is observed to apply to the annotated gene product." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_obsolete: true
[Typedef]
id: depends_on
name: depends on
xref: RO:0002502
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso BFO:0000169
[Typedef]
id: developmentally_related_to
name: developmentally related to
def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" []
xref: RO:0002324
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string
[Typedef]
id: directly_negatively_regulates
name: directly negatively regulates
def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002630
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range BFO:0000015 xsd:string
is_a: directly_regulates ! directly regulates
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: negatively_regulates ! negatively regulates
[Typedef]
id: directly_positively_regulates
name: directly positively regulates
def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002629
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range BFO:0000015 xsd:string
is_a: directly_regulates ! directly regulates
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: positively_regulates ! positively regulates
[Typedef]
id: directly_regulates
name: directly regulates
def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002578
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly regulates (processual)" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range BFO:0000015 xsd:string
property_value: RO:0002575 RO:0002211
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: immediately_causally_upstream_of ! immediately causally upstream of
is_a: regulates ! regulates
[Typedef]
id: during
name: during
namespace: go/extensions/gorel
xref: GOREL:0000002
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "BFO:0000007 WBls:0000075 ZFS:0100000" xsd:string
property_value: usage "Identifies a process or life stage during which a molecular function or biological process occurs or a cellular component is present" xsd:string
range: BFO:0000015
is_transitive: true
[Typedef]
id: during_which_ends
name: 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.
subset: ro-eco
xref: RO:0002084
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: temporally_related_to ! temporally related to
inverse_of: ends_during ! ends during
[Typedef]
id: during_which_starts
name: 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.
subset: ro-eco
xref: RO:0002088
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: temporally_related_to ! temporally related to
inverse_of: starts_during ! starts during
[Typedef]
id: ecologically_related_to
name: ecologically related to
def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" []
subset: ro-eco
xref: RO:0002321
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string
[Typedef]
id: enabled_by
name: enabled by
def: "inverse of enables" []
xref: RO:0002333
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: functionally_related_to ! functionally related to
[Typedef]
id: enables
name: enables
xref: RO:0002327
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
property_value: 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." xsd:string
property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string
is_a: capable_of ! capable of
is_a: go_annotation_extension_relation ! go annotation extension relation
inverse_of: enabled_by ! enabled by
[Typedef]
id: enables_activity_in
name: enables activity in
def: "c executes activity in d if and only if c enables p and p occurs_in d" []
xref: RO:0002432
property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "executes activity in" xsd:string
holds_over_chain: enables occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: functionally_related_to ! functionally related to
[Typedef]
id: encompasses
name: 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.
xref: RO:0002085
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "di" xsd:string
is_transitive: true
is_a: during_which_starts ! during which starts
inverse_of: happens_during ! happens during
[Typedef]
id: ends_after
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
xref: RO:0002086
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
holds_over_chain: ends_during preceded_by
is_transitive: true
is_a: temporally_related_to ! temporally related to
[Typedef]
id: ends_during
name: 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).
subset: ro-eco
xref: RO:0002093
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "o" xsd:string
property_value: IAO:0000118 "overlaps" xsd:string
is_a: temporally_related_to ! temporally related to
[Typedef]
id: exists_during
name: exists_during
namespace: go/extensions/gorel
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]
subset: AE_biological_process
subset: AE_developmental_stages
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "during" BROAD RO:0008000 [PomBase:curators]
xref: GOREL:0000032
property_value: local_domain BFO:0000004 xsd:string
property_value: local_range "GO:0008150 WBls:0000075 ZFS:0100000" xsd:string
property_value: usage "Identifies a process or life stage during which a cellular component is present" xsd:string
domain: BFO:0000004
range: BFO:0000015
is_a: during ! during
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: exports
name: exports
namespace: go/extensions/gorel
alt_id: GOREL:0000035
xref: RO:0002345
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: transports_or_maintains_localization_of ! transports or maintains localization of
transitive_over: has_part ! has part
[Typedef]
id: formed_as_result_of
name: formed as result of
xref: RO:0002354
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: output_of ! output of
[Typedef]
id: functionally_related_to
name: functionally related to
xref: RO:0002328
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string
[Typedef]
id: gene_product_of
name: gene product of
namespace: go/extensions/gorel
alt_id: GOREL:0001028
def: "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\"" []
xref: RO:0002204
property_value: IAO:0000114 IAO:0000125
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: local_domain BFO:0000004 xsd:string
property_value: local_range BFO:0000002 xsd:string
property_value: 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." xsd:string
domain: BFO:0000004
range: BFO:0000002
is_a: genomically_related_to ! genomically related to
is_a: go_annotation_extension_relation ! go annotation extension relation
inverse_of: has_gene_product ! has gene product
[Typedef]
id: genomically_related_to
name: genomically related to
def: "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." []
xref: RO:0002330
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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" xsd:string
domain: BFO:0000002
range: BFO:0000002
[Typedef]
id: go_annotation_extension_relation
name: go annotation extension relation
xref: GOREL:0000000
[Typedef]
id: happens_during
name: happens during
namespace: go/extensions/gorel
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))
subset: AE_biological_process
subset: AE_developmental_stages
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
synonym: "during" BROAD RO:0008000 [PomBase:curators]
synonym: "occurs_during" EXACT [GOC:mah]
xref: RO:0002092
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "d" xsd:string
property_value: IAO:0000118 "during" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "GO:0008150 WBls:0000075 ZFS:0100000 UBERON:0000105" xsd:string
property_value: 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." xsd:string
is_transitive: true
is_a: during ! during
is_a: ends_during ! ends during
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: has_agent
name: has active participant
namespace: go/extensions/gorel
alt_id: GOREL:0001007
def: "x has participant y if and only if x realizes some active role that inheres in y" []
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.
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0002218
property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has agent" xsd:string
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
[Typedef]
id: has_causal_agent
name: has causal agent
def: "Inverse of 'causal agent in'" []
xref: RO:0002608
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: causally_related_to ! causally related to
[Typedef]
id: has_direct_input
name: has_direct_input
namespace: go/extensions/gorel
alt_id: directly_localizes
alt_id: GOREL:0000019
alt_id: GOREL:0000504
alt_id: has_direct_target
alt_id: has_substrate
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]
subset: AE_chemical
subset: AE_sequence_or_complex
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "directly_localizes" NARROW [GOC:ecd]
synonym: "has_direct_target" EXACT [GOC:ecd]
synonym: "has_substrate" NARROW [GOC:ecd]
xref: GOREL:0000752
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697 SO:0000839" xsd:string
property_value: 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." xsd:string
domain: BFO:0000015
is_a: has_input ! has input
[Typedef]
id: has_downstream_target
name: has_downstream_target
namespace: go/extensions/gorel
xref: GOREL:0000022
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
is_obsolete: true
[Typedef]
id: has_end_location
name: has end location
def: "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" []
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0002232
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "ends with process that occurs in" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1" xsd:string
property_value: 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'." xsd:string
domain: BFO:0000015
range: BFO:0000004
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_part_that_occurs_in ! has part that occurs in
[Typedef]
id: has_gene_product
name: has gene product
def: "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" []
xref: RO:0002205
property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string
property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000002
range: BFO:0000004
is_a: genomically_related_to ! genomically related to
[Typedef]
id: has_host
name: has host
subset: ro-eco
subset: taxon_extension
xref: RO:0002454
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: symbiotically_interacts_with ! symbiotically interacts with
[Typedef]
id: has_indirect_input
name: has_indirect_input
namespace: go/extensions/gorel
alt_id: GOREL:0000505
alt_id: has_indirect_target
alt_id: indirectly_localizes
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]
synonym: "has_indirect_target" EXACT [GOC:ecd]
synonym: "indirectly_localizes" NARROW [GOC:ecd]
xref: GOREL:0000751
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
property_value: usage "Identifies an entity indirectly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in MF or BP." xsd:string
is_obsolete: true
[Typedef]
id: has_input
name: has input
namespace: go/extensions/gorel
alt_id: GOREL:0000016
alt_id: GOREL:0000503
alt_id: has_target
alt_id: localizes
def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
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.
subset: AE_chemical
subset: AE_sequence_or_complex
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
synonym: "has_target" EXACT [GOC:ecd]
synonym: "localizes" NARROW [GOC:ecd]
xref: GOREL:0000753
xref: RO:0002233
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697 SO:0000839 NCBITaxon:1" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
inverse_of: input_of ! input of
[Typedef]
id: has_output
name: has output
namespace: go/extensions/gorel
def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." []
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." []
subset: AE_chemical
subset: AE_sequence_or_complex
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0002234
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "produces" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697" xsd:string
property_value: usage "Identifies an entity that is changed or created after participation in a molecular function or biological process" xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
inverse_of: output_of ! output of
[Typedef]
id: has_output_o_axis_of
name: has_output_o_axis_of
namespace: go/extensions/gorel
def: "This is the combination of the has_output relation with the axis_of relation" [GOC:cjm, GOC:dph, GOC:mtg_berkeley_2012_08_27]
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
xref: GOREL:0001002
property_value: usage "This is the combination of the has_output relation with the axis_of relation" xsd:string
equivalent_to_chain: has_output axis_of ! axis_of
[Typedef]
id: has_output_o_product_of
name: has_output_o_product_of
namespace: go/extensions/gorel
def: "This is the combination of the has_output relation with the gene_product_of relation." [GOC:mtg_berkeley_2013]
xref: GOREL:0001029
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "PR:000000001 SO:0000673" xsd:string
property_value: usage "This is the combination of the has_output relation with the results_in_specification_of relation." xsd:string
domain: BFO:0000015
equivalent_to_chain: has_output gene_product_of ! gene product of
[Typedef]
id: has_part
name: has part
namespace: go/extensions/gorel
def: "a core relation that holds between a whole and its part" []
synonym: "has part" EXACT RO:0008000 [PomBase:curators]
xref: BFO:0000051
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: 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." xsd:string
property_value: 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 https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: 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.)\n\nA 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'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
is_a: overlaps ! overlaps
[Typedef]
id: has_part_structure_that_is_capable_of
name: has part structure that is capable of
def: "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" []
xref: RO:0002584
property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: has_part capable_of
is_a: causal_relation_between_material_entity_and_a_process ! causal relation between material entity and a process
is_a: functionally_related_to ! functionally related to
[Typedef]
id: has_part_that_occurs_in
name: has part that occurs in
def: "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." []
subset: ro-eco
xref: RO:0002479
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000003
range: BFO:0000004
holds_over_chain: has_part occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"}
[Typedef]
id: has_participant
name: has participant
namespace: go/extensions/gorel
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
comment: Do not use this relation directly
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0000057
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: 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." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CARO:0000000" xsd:string
property_value: usage "Identifies an entity affected by the gene product's participation in a molecular function or biological process" xsd:string
domain: BFO:0000003
range: BFO:0000002
holds_over_chain: has_part has_participant
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: has_pathogen
name: has pathogen
subset: ro-eco
subset: taxon_extension
xref: RO:0002557
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: host_of ! host of
[Typedef]
id: has_regulation_target
name: has_regulation_target
namespace: go/extensions/gorel
comment: probably want to add one or two new subtypes that capture something about directness
subset: AE_sequence_or_complex
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates" BROAD RO:0008000 []
xref: GOREL:0000015
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697" xsd:string
property_value: usage "Use this relationship to link a regulatory process or function to an entity that (such as a gene, gene product, or complex) participates in the regulated process. This is a very general relation. Use something more specific wherever possible, e.g. 'regulates expression of' or 'regulates transport of'." xsd:string
domain: BFO:0000015
range: BFO:0000002
holds_over_chain: regulates has_participant
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
[Typedef]
id: has_start_location
name: has start location
def: "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" []
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0002231
property_value: display_for_curators "" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "starts with process that occurs in" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1" xsd:string
property_value: 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." xsd:string
domain: BFO:0000015
range: BFO:0000004
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_part_that_occurs_in ! has part that occurs in
[Typedef]
id: has_target_anatomical_entity
name: has_target_anatomical_entity
namespace: go/extensions/gorel
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.
xref: GOREL:0000007
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range CARO:0000000 xsd:string
domain: BFO:0000001
range: CARO:0000000
is_obsolete: true
consider: has_input
consider: has_output
[Typedef]
id: has_target_cell
name: has_target_cell
namespace: go/extensions/gorel
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.
xref: GOREL:0000006
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
domain: BFO:0000001
range: CL:0000000
is_obsolete: true
consider: has_input
consider: has_output
[Typedef]
id: has_target_end_location
name: has target end location
def: "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." []
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002339
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: local_range "GO:0005575 CL:0000000 UBERON:0001062" xsd:string
property_value: usage "Use to relate a transport or localization process to the end location of the transported or localized cargo." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: results_in_transport_to_from_or_in ! results in transport to from or in
transitive_over: part_of ! part of
[Typedef]
id: has_target_start_location
name: has target start location
def: "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." []
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002338
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: local_range "GO:0005575 CL:0000000 UBERON:0001062" xsd:string
property_value: usage "Use to relate a transport or localization process to the starting location of the cargo." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: results_in_transport_to_from_or_in ! results in transport to from or in
transitive_over: part_of ! part of
[Typedef]
id: has_upstream_or_downstream_target
name: has_upstream_or_downstream_target
namespace: go/extensions/gorel
xref: GOREL:0000020
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
domain: GO:0008150
is_obsolete: true
[Typedef]
id: has_upstream_target
name: has_upstream_target
namespace: go/extensions/gorel
xref: GOREL:0000021
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
domain: GO:0008150
is_obsolete: true
[Typedef]
id: host_of
name: host of
subset: ro-eco
subset: taxon_extension
xref: RO:0002453
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: symbiotically_interacts_with ! symbiotically interacts with
[Typedef]
id: hyperparasite_of
name: hyperparasite of
def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" []
subset: ro-eco
synonym: "epiparasite of" RELATED []
synonym: "hyperparasitoid of" RELATED []
xref: RO:0002553
property_value: 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" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string
holds_over_chain: parasite_of parasite_of
is_a: has_host ! has host
inverse_of: hyperparasitized_by ! hyperparasitized by
[Typedef]
id: hyperparasitized_by
name: hyperparasitized by
def: "inverse of hyperparasite of" []
subset: ro-eco
subset: RO:0002259
synonym: "has epiparasite" RELATED []
synonym: "has hyperparasite" RELATED []
synonym: "hyperparasitoidized by" RELATED []
xref: RO:0002554
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: parasitized_by parasitized_by
is_a: host_of ! host of
[Typedef]
id: immediately_causally_downstream_of
name: immediately causally downstream of
xref: RO:0002405
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: causally_downstream_of ! causally downstream of
is_a: immediately_preceded_by ! immediately preceded by
inverse_of: immediately_causally_upstream_of ! immediately causally upstream of
[Typedef]
id: immediately_causally_upstream_of
name: immediately causally upstream of
def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." []
xref: RO:0002412
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0002575 RO:0002411
is_a: causally_upstream_of ! causally upstream of
is_a: immediately_precedes ! immediately precedes
[Typedef]
id: immediately_preceded_by
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
xref: RO:0002087
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
is_a: preceded_by ! preceded by
inverse_of: immediately_precedes ! immediately precedes
[Typedef]
id: immediately_precedes
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
xref: RO:0002090
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
is_a: precedes ! precedes
[Typedef]
id: imports
name: imports
namespace: go/extensions/gorel
alt_id: GOREL:0000034
def: "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." []
xref: RO:0002340
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: transports_or_maintains_localization_of ! transports or maintains localization of
transitive_over: has_part ! has part
[Typedef]
id: in_absence_of
name: in_absence_of
namespace: go/extensions/gorel
def: "Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product." [GOC:rph]
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.
subset: AE_chemical
subset: AE_sequence_or_complex
subset: valid_for_annotation_extension
xref: GOREL:0000755
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
property_value: 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." xsd:string
domain: BFO:0000001
[Typedef]
id: in_presence_of
name: in_presence_of
namespace: go/extensions/gorel
def: "Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product." [GOC:mah]
subset: AE_chemical
subset: AE_sequence_or_complex
subset: valid_for_annotation_extension
synonym: "in presence of" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000027
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
property_value: 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." xsd:string
domain: BFO:0000001
[Typedef]
id: independent_of
name: independent_of
namespace: go/extensions/gorel
alt_id: not_dependent_on
def: "Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product." [GOA:rph]
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.
subset: AE_biological_process
subset: AE_chemical
subset: AE_molecular_function
subset: AE_sequence_feature
subset: AE_sequence_or_complex
synonym: "independent_of" EXACT [GOC:rph]
synonym: "not dependent on" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000013
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "CHEBI:24431 GO:0003674 GO:0005575 GO:0008150 GO:0032991 MI:0315 MOD:00000 PR:000000001 SO:0000110 SO:0000673 SO:0000704" xsd:string
property_value: usage "Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product." xsd:string
domain: BFO:0000001
[Typedef]
id: inheres_in
name: inheres in
def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" []
xref: RO:0000052
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string
property_value: IAO:0000112 "this red color inheres in this apple" xsd:string
property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_a: inheres_in_part_of ! inheres in part of
inverse_of: bearer_of ! bearer of
[Typedef]
id: inheres_in_part_of
name: inheres in part of
def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." []
xref: RO:0002314
property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
property_value: RO:0001900 RO:0001901
holds_over_chain: inheres_in part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: depends_on ! depends on
transitive_over: part_of ! part of
[Typedef]
id: inhibited_by
name: inhibited_by
namespace: go/extensions/gorel
def: "Identifies a chemical substance that decreases the activity of the gene product." [GOC:mah]
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.
subset: AE_chemical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "activity_decreased_by" EXACT [GOC:mah]
synonym: "inhibited by" EXACT RO:0008000 [PomBase:curators]
synonym: "inhibited_by_chemical" EXACT [GOC:mah]
synonym: "inhibited_by_substance" EXACT [GOC:mah]
xref: GOREL:0000508
property_value: local_domain GO:0003674 xsd:string
property_value: local_range CHEBI:24431 xsd:string
property_value: usage "Identifies a chemical substance that decreases the activity of the gene product." xsd:string
domain: GO:0003674
range: CHEBI:24431
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: inhibits_protease
name: inhibits_protease
namespace: go/extensions/gorel
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.
xref: GOREL:0000014
property_value: local_domain GO:0010466 xsd:string
property_value: local_range "PR:000000001 SO:0000673" xsd:string
property_value: usage "OBSOLETE. Identifies a specific target of regulation of a MF" xsd:string
domain: GO:0010466
is_obsolete: true
[Typedef]
id: input_of
name: input of
def: "inverse of has input" []
subset: ro-eco
subset: RO:0002259
xref: RO:0002352
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: functionally_related_to ! functionally related to
is_a: participates_in ! participates in
[Typedef]
id: interacts_with
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
subset: ro-eco
synonym: "in pairwise interaction with" EXACT []
xref: RO:0002434
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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." xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI
domain: BFO:0000040
range: BFO:0000040
is_symmetric: true
[Typedef]
id: interacts_with_via_parasite-host_interaction
name: interacts with via parasite-host interaction
def: "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)." []
subset: ro-eco
xref: RO:0002443
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI
property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string
property_value: RO:0002561 GO:0072519
is_a: symbiotically_interacts_with ! symbiotically interacts with
[Typedef]
id: involved_in
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
xref: RO:0002331
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
holds_over_chain: enables part_of
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of
transitive_over: part_of ! part of
[Typedef]
id: involved_in_negative_regulation_of
name: involved in negative regulation of
xref: RO:0002430
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: enables negatively_regulates
holds_over_chain: involved_in negatively_regulates
is_a: involved_in_regulation_of ! involved in regulation of
[Typedef]
id: involved_in_or_involved_in_regulation_of
name: involved in or involved in regulation of
def: "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" []
xref: RO:0002431
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "involved in or reguates" xsd:string
is_a: acts_upstream_of_or_within ! acts upstream of or within
is_a: causal_agent_in ! causal agent in
is_a: functionally_related_to ! functionally related to
[Typedef]
id: involved_in_positive_regulation_of
name: involved in positive regulation of
xref: RO:0002429
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: enables positively_regulates
holds_over_chain: involved_in positively_regulates
is_a: involved_in_regulation_of ! involved in regulation of
[Typedef]
id: involved_in_regulation_of
name: involved in regulation of
def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" []
xref: RO:0002428
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: enables regulates
holds_over_chain: involved_in regulates
is_a: acts_upstream_of ! acts upstream of
is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of
[Typedef]
id: localization_dependent_on
name: localization_dependent_on
namespace: go/extensions/gorel
def: "Identifies a requirement under which the gene product is located at the specified cellular component." [GOC:rph]
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]
subset: AE_biological_process
subset: AE_cellular_component
subset: AE_chemical
subset: AE_molecular_function
subset: AE_sequence_feature
subset: AE_sequence_or_complex
synonym: "localized by" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000009
property_value: local_domain GO:0005575 xsd:string
property_value: local_range "CHEBI:24431 GO:0003674 GO:0005575 GO:0008150 GO:0032991 MI:0315 MOD:00000 PR:000000001 SO:0000110 SO:0000673 SO:0000704" xsd:string
property_value: usage "Identifies a requirement under which the gene product is located at the specified cellular component." xsd:string
domain: GO:0005575
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: localizes_to
name: localizes_to
namespace: go/extensions/gorel
def: "OBSOLETE. c localizes_to d if c executes some function when it is part_of d." [BFO:cjm]
comment: TODO : check this one. Note Pombe is using different variant.
synonym: "localization_destination" EXACT [GOC:mah]
xref: GOREL:0000003
property_value: local_domain BFO:0000004 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: usage "OBSOLETE. c localizes_to d if c executes some function when it is part_of d." xsd:string
domain: BFO:0000004
transitive_over: part_of ! part of
is_obsolete: true
[Typedef]
id: mereotopologically_related_to
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
xref: RO:0002323
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: 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" xsd:string
property_value: RO:0001900 RO:0001901
[Typedef]
id: modified_by
name: modified_by
namespace: go/extensions/gorel
def: "Identifies the gene product that catalyzes a modification on the annotated gene product" [GOC:mah]
synonym: "modified by" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000030
property_value: local_domain MOD:00000 xsd:string
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
property_value: usage "Identifies the gene product that catalyzes a modification on the annotated gene product" xsd:string
domain: MOD:00000
[Typedef]
id: molecularly_controls
name: molecularly controls
def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" []
xref: RO:0002448
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: causally_influences ! causally influences
is_a: molecularly_interacts_with ! molecularly interacts with
[Typedef]
id: molecularly_interacts_with
name: molecularly interacts with
def: "An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected." []
xref: RO:0002436
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "binds" xsd:string
property_value: IAO:0000118 "molecularly binds with" xsd:string
property_value: seeAlso ECO:0000353
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI
is_symmetric: true
is_a: interacts_with ! interacts with
[Typedef]
id: negatively_regulated_by
name: negatively regulated by
def: "inverse of negatively regulates" []
subset: RO:0002259
xref: RO:0002335
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: regulated_by ! regulated by
[Typedef]
id: negatively_regulates
name: negatively regulates
def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002212
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range BFO:0000015 xsd:string
is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates ! regulates
inverse_of: negatively_regulated_by ! negatively regulated by
[Typedef]
id: not_during
name: not_during
namespace: go/extensions/gorel
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
synonym: "except during" BROAD RO:0008000 [PomBase:curators]
xref: GOREL:0000024
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "BFO:0000007 WBls:0000075 ZFS:0100000" xsd:string
property_value: 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)." xsd:string
domain: BFO:0000001
range: BFO:0000007
is_class_level: true
[Typedef]
id: not_exists_during
name: not_exists_during
namespace: go/extensions/gorel
def: "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)." [GOC:mah]
synonym: "does_not_exist_during" EXACT [GOC:mah]
synonym: "except during" BROAD RO:0008000 [PomBase:curators]
xref: GOREL:0000026
property_value: local_domain BFO:0000004 xsd:string
property_value: local_range "BFO:0000007 WBls:0000075 ZFS:0100000" xsd:string
property_value: 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)." xsd:string
domain: BFO:0000004
range: BFO:0000007
is_a: not_during ! not_during
is_class_level: true
[Typedef]
id: not_happens_during
name: not_happens_during
namespace: go/extensions/gorel
def: "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)." [GOC:mah]
synonym: "does_not_happen_during" EXACT [GOC:mah]
synonym: "except during" BROAD RO:0008000 [PomBase:curators]
synonym: "not_occurs_during" EXACT [GOC:mah]
xref: GOREL:0000025
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "BFO:0000007 WBls:0000075 ZFS:0100000" xsd:string
property_value: 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)." xsd:string
domain: BFO:0000007
range: BFO:0000007
is_a: not_during ! not_during
is_class_level: true
[Typedef]
id: not_occurs_at
name: not_occurs_at
namespace: go/extensions/gorel
def: "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." [GOC:mah]
synonym: "not at" RELATED RO:0008000 [PomBase:curators]
xref: GOREL:0000509
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "GO:0005575 SO:0000110" xsd:string
property_value: usage "An entity (e.g. Cellular Component, sequence feature) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at." xsd:string
domain: BFO:0000007
is_class_level: true
[Typedef]
id: not_occurs_in
name: not_occurs_in
namespace: go/extensions/gorel
def: "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." [GOC:mah]
synonym: "not in" RELATED RO:0008000 [PomBase:curators]
xref: GOREL:0000506
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
domain: BFO:0000007
is_class_level: true
[Typedef]
id: occurs_at
name: occurs at
namespace: go/extensions/gorel
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.
subset: AE_cellular_component
subset: AE_sequence_feature
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "at" RELATED RO:0008000 [PomBase:curators]
xref: GOREL:0000501
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "GO:0005575 SO:0000110" xsd:string
property_value: usage "Identifies the Cellular Component or sequence feature adjacent to or in the vicinity of which the Molecular Function or Biological Process is executed" xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: occurs_in
name: occurs in
namespace: go/extensions/gorel
def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between 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]
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "in" RELATED RO:0008000 [PomBase:curators]
xref: BFO:0000066
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1" xsd:string
property_value: usage "Identifies the cell, tissue, cellular component or anatomical entity within which all parts of the molecular function or biological process occurs" xsd:string
domain: BFO:0000003
range: BFO:0000004
holds_over_chain: part_of occurs_in
is_a: go_annotation_extension_relation ! go annotation extension relation
inverse_of: contains_process ! contains process
transitive_over: part_of ! part of
[Typedef]
id: output_of
name: output of
def: "inverse of has output" []
subset: ro-eco
subset: RO:0002259
xref: RO:0002353
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: functionally_related_to ! functionally related to
is_a: participates_in ! participates in
[Typedef]
id: overlaps
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: ro-eco
xref: RO:0002131
property_value: IAO:0000114 IAO:0000125
property_value: RO:0001900 RO:0001901
holds_over_chain: has_part overlaps
holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: part_of part_of
is_a: mereotopologically_related_to ! mereotopologically related to
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
[Typedef]
id: parasite_of
name: parasite of
subset: ro-eco
subset: taxon_extension
synonym: "direct parasite of" EXACT []
xref: RO:0002444
property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "parasitizes" xsd:string
property_value: RO:0002560 GO:0072519
property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_host ! has host
is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction
inverse_of: parasitized_by ! parasitized by
[Typedef]
id: parasitized_by
name: parasitized by
subset: ro-eco
synonym: "directly parasitized by" EXACT []
xref: RO:0002445
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has parasite" xsd:string
property_value: IAO:0000118 "parasitised by" xsd:string
property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string
is_a: host_of ! host of
is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction
[Typedef]
id: part_of
name: part of
namespace: go/extensions/gorel
def: "a core relation that holds between a part and its whole" []
subset: AE_biological_process
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: AE_developmental_stages
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "part of" EXACT RO:0008000 [PomBase:curators]
xref: BFO:0000050
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: 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." xsd:string
property_value: 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 https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: 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.)\n\nA 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'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range "CL:0000000 GO:0005575 GO:0008150 PO:0009012 PO:0025131 UBERON:0001062 ZFS:0100000 WBls:0000075 WBbt:0004017 WBbt:0005766 NCBITaxon:1" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
property_value: 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." xsd:string
is_transitive: true
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: overlaps ! overlaps
inverse_of: has_part ! has part
[Typedef]
id: part_of_structure_that_is_capable_of
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
xref: RO:0002329
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: functionally_related_to ! functionally related to
[Typedef]
id: participates_in
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
xref: RO:0000056
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
domain: BFO:0000002
range: BFO:0000003
inverse_of: has_participant ! has participant
[Typedef]
id: participates_in_a_biotic-biotic_interaction_with
name: participates in a biotic-biotic interaction with
subset: ro-eco
xref: RO:0002574
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005
is_a: biotically_interacts_with ! biotically interacts with
[Typedef]
id: pathogen_of
name: pathogen of
subset: ro-eco
subset: taxon_extension
xref: RO:0002556
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_host ! has host
inverse_of: has_pathogen ! has pathogen
[Typedef]
id: positively_regulated_by
name: positively regulated by
def: "inverse of positively regulates" []
subset: RO:0002259
xref: RO:0002336
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: regulated_by ! regulated by
[Typedef]
id: positively_regulates
name: positively regulates
def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002213
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range BFO:0000015 xsd:string
holds_over_chain: negatively_regulates negatively_regulates
is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates ! regulates
inverse_of: positively_regulated_by ! positively regulated by
[Typedef]
id: preceded_by
name: preceded by
def: "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." []
subset: ro-eco
xref: BFO:0000062
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: 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." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
domain: BFO:0000003
range: BFO:0000003
holds_over_chain: happens_during preceded_by
holds_over_chain: part_of preceded_by
holds_over_chain: starts_during preceded_by
is_transitive: true
is_a: ends_after ! ends after
inverse_of: precedes ! precedes
[Typedef]
id: precedes
name: precedes
def: "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." []
subset: ro-eco
xref: BFO:0000063
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003
range: BFO:0000003
holds_over_chain: happens_during precedes
holds_over_chain: part_of precedes
is_transitive: true
is_a: temporally_related_to ! temporally related to
[Typedef]
id: produced_by
name: produced by
def: "a produced_by b iff some process that occurs_in b has_output a." []
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0003001
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Melissa Haendel" xsd:string
property_value: local_domain GO:0005575 xsd:string
property_value: local_range CL:0000000 xsd:string
property_value: 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." xsd:string
domain: BFO:0000040
range: BFO:0000040
[Typedef]
id: produces
name: produces
def: "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." []
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.
subset: ro-eco
xref: RO:0003000
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Melissa Haendel" xsd:string
domain: BFO:0000040
range: BFO:0000040
inverse_of: produced_by ! produced by
[Typedef]
id: protease_activator
name: protease_activator
namespace: go/extensions/gorel
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.
xref: GOREL:0000017
property_value: local_domain GO:0010952 xsd:string
property_value: local_range "PR:000000001 SO:0000673" xsd:string
property_value: usage "OBSOLETE. Identifies a specific target of regulation of a MF" xsd:string
domain: GO:0010952
is_obsolete: true
[Typedef]
id: regulated_by
name: regulated by
def: "inverse of regulates" []
subset: RO:0002259
xref: RO:0002334
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
domain: BFO:0000015
range: BFO:0000015
is_transitive: true
is_a: causally_downstream_of_or_within ! causally downstream of or within
[Typedef]
id: regulates
name: regulates
def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" []
subset: AE_biological_process
subset: AE_molecular_function
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002211
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range BFO:0000015 xsd:string
domain: BFO:0000015
range: BFO:0000015
holds_over_chain: directly_regulates directly_regulates
is_transitive: true
is_a: causally_upstream_of ! causally upstream of
is_a: go_annotation_extension_relation ! go annotation extension relation
inverse_of: regulated_by ! regulated by
[Typedef]
id: regulates_activity_of
name: regulates activity of
def: "A relation that holds between the regulation of a molecular function and the agent that executes that function." []
subset: AE_sequence_or_complex
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0098702
property_value: local_domain "GO:0098772 GO:0065009" xsd:string
property_value: local_range "GO:0043234 SO:0000374 PR:000000001" xsd:string
property_value: 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." xsd:string
is_a: regulates_o_has_agent ! regulates_o_has_agent
[Typedef]
id: regulates_expression_of
name: regulates expression of
def: "A relationship that holds between a process and a gene whose expression is regulated by that process." []
subset: AE_sequence_feature
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0098789
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range SO:0000704 xsd:string
property_value: usage "Relates a regulatory process or function to the gene whose expression it regulates. Expression encompasses transcription, regulation and processing involved in maturation." xsd:string {xref="GOC:dos"}
domain: BFO:0000015
range: SO:0000704
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_input ! regulates_o_has_input
[Typedef]
id: regulates_level_of
name: regulates levels of
namespace: go/extensions/gorel
alt_id: GOREL:0000036
def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" []
xref: RO:0002332
property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string
is_a: functionally_related_to ! functionally related to
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: regulates_o_acts_on_population_of
name: regulates process that acts on population of
namespace: go/extensions/gorel
def: "A relation that applies between a regulatory process and a population of entities that a process it regulates acts on." [GOC:mtg_berkeley_2013]
synonym: "regulates_o_acts_on_population_of" EXACT []
xref: GOREL:0001008
property_value: IAO:0000112 "'positive regulation of cell proliferation' and 'regulates process that acts on population of' some 'stem cell'" xsd:string
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "CL:0000000 GO:0005575 WBbt:0004017" xsd:string
property_value: usage "This is the combination of the regulates relation with the acts_on_population_of relation." xsd:string
domain: BFO:0000015
is_a: has_regulation_target ! has_regulation_target
equivalent_to_chain: regulates acts_on_population_of ! acts_on_population_of
[Typedef]
id: regulates_o_has_agent
name: regulates_o_has_agent
namespace: go/extensions/gorel
def: "A relationship between the regulation of a process and the agent that executes that process." [GOC:dos]
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates_o_has_agent" EXACT []
xref: GOREL:0001011
property_value: local_domain "GO:0098772 GO:0065009" xsd:string
property_value: local_range "PO:0025131 GO:0043234 SO:0000374 UBERON:0000465 SO:0000374 PR:000000001" xsd:string
domain: BFO:0000015
range: BFO:0000004
is_a: has_regulation_target ! has_regulation_target
equivalent_to_chain: regulates has_agent ! has active participant
[Typedef]
id: regulates_o_has_input
name: regulates_o_has_input
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the has_input relation" [GOC:dph]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001030
property_value: usage "This is the combination of the regulates relation with the has_input relation" xsd:string
domain: BFO:0000015
is_a: has_regulation_target ! has_regulation_target
equivalent_to_chain: regulates has_input ! has input
[Typedef]
id: regulates_o_has_output
name: regulates_o_has_output
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the has_output relation" [GOC:cjm, GOC:dph, GOC:mtg_berkeley_2012_08_27]
xref: GOREL:0001003
property_value: usage "This is the combination of the regulates relation with the has_output relation" xsd:string
domain: BFO:0000015
is_a: has_regulation_target ! has_regulation_target
equivalent_to_chain: regulates has_output ! has output
[Typedef]
id: regulates_o_has_participant
name: regulates_o_has_participant
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the has_participant relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001016
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 GO:0008150 PO:0009012 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: usage "Use this relationship to link a regulatory process or function to an entity that participates in the regulated process." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
[Typedef]
id: regulates_o_occurs_in
name: regulates process that occurs in
namespace: go/extensions/gorel
def: "A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in." [GOC:cjm, GOC:dph, GOC:mtg_berkeley_2012_08_27]
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates_o_occurs_in" EXACT []
xref: GOREL:0001004
property_value: IAO:0000112 "'negative regulation of chromosome segregation' that regulates_o_occurs_in some spermatocyte." xsd:string
property_value: local_domain GO:0065007 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: usage "Use this relation to link a regulatory process or function to the structure that the regulated process or function occurs in." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
equivalent_to_chain: regulates occurs_in ! occurs in
[Typedef]
id: regulates_o_results_in_acquisition_of_features_of
name: regulates acquisition of features of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_acquisition_of_features_of relation." [GOC:mtg_berkeley_2013]
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates differentiation of" EXACT []
synonym: "regulates_o_results_in_acquisition_of_features_of" EXACT []
xref: GOREL:0001010
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 PO:0009002 1 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
domain: BFO:0000015
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_acquisition_of_features_of ! results in acquisition of features of
[Typedef]
id: regulates_o_results_in_commitment_to
name: regulates commitment to
namespace: go/extensions/gorel
def: "A relation that applies between a process that regulates cell fate commitment and the cell type that the regulated process results in commitment to." [GOC:mtg_berkeley_2013]
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates_o_results_in_commitment_to" EXACT []
xref: GOREL:0001022
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_commitment_to relation." xsd:string
domain: GO:0010453
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_commitment_to ! results in commitment to
[Typedef]
id: regulates_o_results_in_development_of
name: regulates development of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_development_of relation." [GOC:mtg_berkeley_2013]
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates_o_results_in_development_of" EXACT []
xref: GOREL:0001023
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
domain: GO:0050793
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_development_of ! results in development of
[Typedef]
id: regulates_o_results_in_division_of
name: regulates division of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_division_of relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001024
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_division_of relation." xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_division_of ! results_in_division_of
[Typedef]
id: regulates_o_results_in_formation_of
name: regulates formation of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_formation_of relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001025
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_formation_of relation." xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_formation_of ! results in formation of
[Typedef]
id: regulates_o_results_in_maturation_of
name: regulates maturation of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_maturation_of relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001012
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0009012 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_maturation_of relation." xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_maturation_of ! results in maturation of
[Typedef]
id: regulates_o_results_in_morphogenesis_of
name: regulates morphogenesis of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_morphogenesis_of relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001026
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_morphogenesis_of relation." xsd:string
domain: GO:0050789
is_a: has_regulation_target ! has_regulation_target
equivalent_to_chain: regulates results_in_morphogenesis_of ! results in morphogenesis of
[Typedef]
id: regulates_o_results_in_movement_of
name: regulates process that results in movement of
namespace: go/extensions/gorel
def: "A relation that holds between a process that regulates locomotion and the cell or organism whose locomotion is being regulated." [GOC:cjm, GOC:dph, GOC:mtg_berkeley_2012_08_27]
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates_o_results_in_movement_of" EXACT []
xref: GOREL:0001005
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 WBbt:0004017" xsd:string
property_value: usage "Use this relation to relate a process that regulates locomotion to the cell or organism whose locomotion is being regulated." xsd:string
domain: GO:0040012
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_movement_of ! results in movement of
[Typedef]
id: regulates_o_results_in_specification_of
name: regulates specification of
namespace: go/extensions/gorel
def: "A relation that applies between a process that regulates the specification of some cell type or structure and the specified cell type or structure." [GOC:mtg_berkeley_2013]
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates_o_results_in_specification_of" EXACT []
xref: GOREL:0001027
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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." xsd:string
domain: GO:0050789
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_specification_of ! results in specification of
[Typedef]
id: regulates_transcription_of
name: regulates transcription of
def: "A relationship that holds between a process and a gene whose transcription is regulated by that process." []
subset: AE_sequence_feature
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0098788
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range SO:0000704 xsd:string
property_value: usage "Relates a regulatory process or function to the gene whose transcription it regulates." xsd:string {xref="GOC:dos"}
domain: BFO:0000015
range: SO:0000704
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_expression_of ! regulates expression of
[Typedef]
id: regulates_translation_of
name: regulates translation of
def: "A relationship that holds between a process and a protein coding gene whose translation is regulated by that process." []
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.
subset: AE_sequence_feature
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0098790
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range SO:0000704 xsd:string
property_value: usage "Relates a regulatory process or function to the gene whose translation it regulates." xsd:string {xref="GOC:dos"}
domain: BFO:0000015
range: SO:0000704
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_expression_of ! regulates expression of
[Typedef]
id: regulates_transport_of
name: regulates transport of
def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." []
subset: AE_chemical
subset: display_for_curators
subset: ro-eco
subset: valid_for_annotation_extension
xref: RO:0002011
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697" xsd:string
property_value: usage "Use this relation to link a process that regulates transport to the the entity being transported." xsd:string
holds_over_chain: regulates transports_or_maintains_localization_of
is_a: regulates_o_has_input ! regulates_o_has_input
[Typedef]
id: related_via_dependence_to
name: related via dependence to
def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." []
xref: RO:0002609
property_value: 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." xsd:string
[Typedef]
id: related_via_localization_to
name: related via localization to
def: "A relationship that holds via some process of localization" []
xref: RO:0002337
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000015
range: BFO:0000002
[Typedef]
id: requires_direct_regulator
name: requires_direct_regulator
namespace: go/extensions/gorel
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)
synonym: "requires direct regulation by" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000033
property_value: 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." xsd:string
domain: GO:0003674
is_obsolete: true
[Typedef]
id: requires_localization
name: requires_localization
namespace: go/extensions/gorel
def: "The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component" [GOC:mah]
synonym: "dependent_on_localization" EXACT [GOC:mah]
synonym: "only when located at" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000028
property_value: local_domain GO:0008150 xsd:string
property_value: local_range GO:0005575 xsd:string
property_value: usage "The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component" xsd:string
domain: GO:0008150
range: GO:0005575
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: requires_modification
name: requires_modification
namespace: go/extensions/gorel
def: "Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process." [GOC:mah]
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
synonym: "only with modification" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000502
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range MOD:00000 xsd:string
property_value: usage "Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process." xsd:string
domain: BFO:0000007
range: MOD:00000
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: requires_regulation_by
name: requires_regulation_by
namespace: go/extensions/gorel
def: "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)" [GOC:mah]
synonym: "requires regulation by" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000029
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
property_value: 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)" xsd:string
domain: BFO:0000007
is_obsolete: true
[Typedef]
id: requires_regulator
name: requires_regulator
namespace: go/extensions/gorel
def: "annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process" [GOC:mah]
synonym: "requires" BROAD RO:0008000 [PomBase:curators]
xref: GOREL:0000011
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704" xsd:string
property_value: usage "annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process" xsd:string
domain: BFO:0000007
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: requires_sequence_feature
name: requires_sequence_feature
namespace: go/extensions/gorel
def: "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." [GOC:mah]
comment: strictly speaking, these fall outside the scope of GO, even with extended annotations
subset: AE_sequence_feature
synonym: "requires" BROAD RO:0008000 [PomBase:curators]
synonym: "requires_feature" BROAD [GOC:mah]
xref: GOREL:0000010
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range SO:0000110 xsd:string
property_value: 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." xsd:string
domain: BFO:0000007
range: SO:0000110
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: requires_substance
name: requires_substance
namespace: go/extensions/gorel
def: " The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance" [GOC:mah]
subset: AE_chemical
synonym: "requires" BROAD RO:0008000 [PomBase:curators]
xref: GOREL:0000012
property_value: local_domain BFO:0000007 xsd:string
property_value: local_range CHEBI:24431 xsd:string
property_value: usage " The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance" xsd:string
domain: BFO:0000007
range: CHEBI:24431
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: requires_target_sequence_feature
name: requires_target_sequence_feature
namespace: go/extensions/gorel
def: "Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process" [GOC:ecd]
synonym: "requires feature in target" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000754
property_value: local_domain BFO:0000001 xsd:string
property_value: local_range SO:0000110 xsd:string
property_value: 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" xsd:string
domain: BFO:0000001
range: SO:0000110
is_a: dependent_on ! dependent_on
is_obsolete: true
[Typedef]
id: results_in_acquisition_of_features_of
name: results in acquisition of features of
namespace: go/extensions/gorel
alt_id: GOREL:0001014
def: "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" []
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "results in differentiation of" EXACT []
xref: RO:0002315
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string
property_value: local_domain GO:0030154 xsd:string
property_value: local_range "CL:0000000 PO:0009002 WBbt:0004017" xsd:string
property_value: usage "Use this relation to link a cell differentiation process to the cell type that the process results in the differentiation of." xsd:string
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_commitment_to
name: results in commitment to
namespace: go/extensions/gorel
alt_id: GOREL:0001017
def: "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." []
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002348
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml#fate xsd:anyURI
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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." xsd:string
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_determination_of
name: results in determination of
namespace: go/extensions/gorel
alt_id: GOREL:0001018
def: "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." []
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002349
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml#fate xsd:anyURI
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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." xsd:string
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_development_of
name: results in development of
namespace: go/extensions/gorel
alt_id: GOREL:0001009
def: "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." []
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.
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002296
property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_developmental_progression_of
name: results in developmental progression of
def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure 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)." []
xref: RO:0002295
property_value: IAO:0000114 IAO:0000125
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso Ontology:extensions
domain: GO:0008150
range: CARO:0000003
is_a: developmentally_related_to ! developmentally related to
[Typedef]
id: results_in_division_of
name: results_in_division_of
namespace: go/extensions/gorel
def: "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." [GOC:mtg_berkeley_2013]
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001019
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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." xsd:string
domain: BFO:0000015
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
[Typedef]
id: results_in_formation_of
name: results in formation of
namespace: go/extensions/gorel
alt_id: GOREL:0001020
def: "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." [GOC:mtg_berkeley_2013]
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002297
property_value: 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." xsd:string
property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_output ! has output
is_a: results_in_developmental_progression_of ! results in developmental progression of
inverse_of: formed_as_result_of ! formed as result of
[Typedef]
id: results_in_maturation_of
name: results in maturation of
namespace: go/extensions/gorel
alt_id: GOREL:0001013
def: "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." []
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.
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002299
property_value: 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" xsd:string
property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0009012 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_morphogenesis_of
name: results in morphogenesis of
namespace: go/extensions/gorel
alt_id: GOREL:0001015
def: "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." []
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.
subset: AE_cell_or_anatomical
subset: AE_cellular_component
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002298
property_value: 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." xsd:string
property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_movement_of
name: results in movement of
namespace: go/extensions/gorel
alt_id: GOREL:0001001
def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" []
comment: For movement of chemicals or cell parts, please use transports_or_maintains_localization_of
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002565
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "" xsd:string
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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." xsd:string
domain: GO:0040011
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
[Typedef]
id: results_in_specification_of
name: results in specification of
namespace: go/extensions/gorel
alt_id: GOREL:0001021
def: "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. " []
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.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: RO:0002356
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml#fate xsd:anyURI
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: 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." xsd:string
domain: GO:0008150
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: results_in_developmental_progression_of ! results in developmental progression of
[Typedef]
id: results_in_transport_to_from_or_in
name: results in transport to from or in
xref: RO:0002344
property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: related_via_localization_to ! related via localization to
[Typedef]
id: spatially_disjoint_from
name: spatially disjoint from
def: "A is spatially_disjoint_from B if and only if they have no parts in common" []
subset: ro-eco
xref: RO:0002163
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: 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. " xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: 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" xsd:string
property_value: RO:0001900 RO:0001901
is_a: mereotopologically_related_to ! mereotopologically related to
expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" []
[Typedef]
id: stabilizes
name: stabilizes
namespace: go/extensions/gorel
def: "Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)" [GOC:mah]
subset: AE_sequence_or_complex
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "stabilizes" EXACT RO:0008000 [PomBase:curators]
xref: GOREL:0000018
property_value: local_domain GO:0031647 xsd:string
property_value: local_range "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697" xsd:string
property_value: usage "Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)" xsd:string
domain: GO:0031647
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_input ! has input
[Typedef]
id: starts_during
name: 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))
subset: ro-eco
xref: RO:0002091
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "io" xsd:string
domain: BFO:0000003
range: BFO:0000003
is_a: temporally_related_to ! temporally related to
[Typedef]
id: symbiotically_interacts_with
name: symbiotically interacts with
def: "A biotic interaction in which the two organisms live together in more or less intimate association." []
subset: ro-eco
xref: RO:0002440
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI
property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string
property_value: RO:0002561 GO:0044403
is_symmetric: true
is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with
[Typedef]
id: temporally_related_to
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
xref: RO:0002222
property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: 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." xsd:string
domain: BFO:0000003
range: BFO:0000003
[Typedef]
id: transcriptionally_regulates
name: transcriptionally_regulates
namespace: go/extensions/gorel
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.
xref: GOREL:0000023
property_value: local_domain GO:0006355 xsd:string
property_value: usage "OBSOLETE. Identifies gene whose transcription is regulated" xsd:string
domain: GO:0006355
is_obsolete: true
replaced_by: has_regulation_target
[Typedef]
id: transports_or_maintains_localization_of
name: transports or maintains localization of
namespace: go/extensions/gorel
def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c" []
subset: AE_cellular_component
subset: AE_chemical
subset: display_for_curators
subset: valid_for_annotation_extension
synonym: "regulates location of" RELATED []
xref: RO:0002313
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "regulates location of" xsd:string
property_value: IAO:0000118 "transports" xsd:string
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697" xsd:string
property_value: 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." xsd:string
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant
is_a: related_via_localization_to ! related via localization to
transitive_over: has_part ! has part