From d6f7977df6759a3e96ad53d6a7d49d712a152c2d Mon Sep 17 00:00:00 2001 From: Saurav Kumar Date: Sun, 3 Sep 2023 11:38:35 +0000 Subject: [PATCH] first release --- pko-base.obo | 13 + pko-base.owl | 84 ++ pko-full.obo | 1375 +++++++++++++++++ pko-full.owl | 4044 ++++++++++++++++++++++++++++++++++++++++++++++++++ pko.obo | 1375 +++++++++++++++++ pko.owl | 4044 ++++++++++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 10935 insertions(+) create mode 100644 pko-base.obo create mode 100644 pko-base.owl create mode 100644 pko-full.obo create mode 100644 pko-full.owl create mode 100644 pko.obo create mode 100644 pko.owl diff --git a/pko-base.obo b/pko-base.obo new file mode 100644 index 0000000..2ac9c60 --- /dev/null +++ b/pko-base.obo @@ -0,0 +1,13 @@ +format-version: 1.2 +data-version: http://si.eu-parc.eu/pko/releases/2023-09-03/pko-base.owl +ontology: http://si.eu-parc.eu/pko/pko-base.owl +property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 +property_value: http://purl.org/dc/terms/description "None" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified +property_value: http://purl.org/dc/terms/title "pharmokinetic-ontology" xsd:string +property_value: owl:versionInfo "2023-09-03" xsd:string + +[Term] +id: PKO:0000000 +name: root node + diff --git a/pko-base.owl b/pko-base.owl new file mode 100644 index 0000000..4bdf32c --- /dev/null +++ b/pko-base.owl @@ -0,0 +1,84 @@ + + + + + + None + + pharmokinetic-ontology + 2023-09-03 + + + + + + + + + + + + + + + + + + + description + + + + + + + + license + + + + + + + + title + + + + + + + + + + + + + root node + + + + + + + diff --git a/pko-full.obo b/pko-full.obo new file mode 100644 index 0000000..3ebb9ee --- /dev/null +++ b/pko-full.obo @@ -0,0 +1,1375 @@ +format-version: 1.2 +data-version: http://si.eu-parc.eu/pko/releases/2023-09-03/pko-full.owl +subsetdef: 3_STAR "" +subsetdef: goslim_agr "" +subsetdef: goslim_candida "" +subsetdef: goslim_chembl "" +subsetdef: goslim_drosophila "" +subsetdef: goslim_flybase_ribbon "" +subsetdef: goslim_generic "" +subsetdef: goslim_metagenomics "" +subsetdef: goslim_mouse "" +subsetdef: goslim_pir "" +subsetdef: goslim_plant "" +subsetdef: goslim_pombe "" +subsetdef: goslim_yeast "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: prokaryote_subset "" +subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +ontology: http://si.eu-parc.eu/pko/pko-full.owl +property_value: dcterms-license https://creativecommons.org/licenses/unspecified +property_value: http://purl.org/dc/terms/description "None" xsd:string +property_value: http://purl.org/dc/terms/title "pharmokinetic-ontology" xsd:string +property_value: owl:versionInfo "2023-09-03" xsd:string + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +relationship: part_of BFO:0000002 {all_only="true"} ! continuant + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: part_of BFO:0000003 {all_only="true"} ! occurrent + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: part_of BFO:0000019 {all_only="true"} ! quality + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: CHEBI:50906 ! role +equivalent_to: CHEBI:50906 ! role + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CHEBI:50906 +name: role +namespace: chebi_ontology +def: "A role is particular behaviour which a material entity may exhibit." [] +subset: 3_STAR +is_a: BFO:0000023 ! role + +[Term] +id: GO:0003674 +name: molecular_function +namespace: molecular_function +alt_id: GO:0005554 +def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] +comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +subset: goslim_candida +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process + +[Term] +id: GO:0003824 +name: catalytic activity +namespace: molecular_function +def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] +subset: goslim_agr +subset: goslim_chembl +subset: goslim_flybase_ribbon +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] +xref: Wikipedia:Enzyme +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. +subset: goslim_candida +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI +created_by: jl +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0016301 +name: kinase activity +namespace: molecular_function +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +synonym: "phosphokinase activity" EXACT [] +xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" +xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups + +[Term] +id: GO:0016740 +name: transferase activity +namespace: molecular_function +def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_mouse +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: prokaryote_subset +xref: EC:2.-.-.- +xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" +xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" +xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK" +xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248" +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +namespace: molecular_function +def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] +comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. +subset: goslim_chembl +xref: EC:2.7.-.- +is_a: GO:0016740 ! transferase activity + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: PKO:0000000 +name: root node + +[Typedef] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +inverse_of: bearer_of ! bearer of + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: has_quality ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: bearer_of ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: bearer_of ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: bearer_of ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +is_a: RO:0000052 ! characteristic of + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +is_a: regulated_by ! regulated by +inverse_of: directly_regulates ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: directly_negatively_regulates ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: directly_positively_regulates ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +is_functional: true +is_a: RO:0002017 ! has component activity +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002222 +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 +property_value: http://purl.org/dc/terms/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 https://orcid.org/0000-0002-6601-2165 +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 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 causally_upstream_of +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 causally_upstream_of_or_within +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002327 +name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +is_a: capable_of ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: has_part ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 part_of +is_a: participates_in ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: has_participant ! has participant + +[Typedef] +id: RO:0002407 +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +holds_over_chain: directly_positively_regulates directly_positively_regulates +holds_over_chain: directly_positively_regulates RO:0002407 +holds_over_chain: RO:0002409 RO:0002409 +is_transitive: true +is_a: positively_regulates ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: directly_positively_regulates ! directly positively regulates + +[Typedef] +id: RO:0002409 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: directly_negatively_regulates directly_negatively_regulates +holds_over_chain: directly_negatively_regulates RO:0002409 +is_transitive: true +is_a: negatively_regulates ! negatively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: directly_negatively_regulates ! directly negatively regulates + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002327 regulates +holds_over_chain: RO:0002331 regulates +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 positively_regulates +holds_over_chain: RO:0002331 positively_regulates +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 negatively_regulates +holds_over_chain: RO:0002331 negatively_regulates +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +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" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002434 +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 [] +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" 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 https://orcid.org/0000-0002-6601-2165 +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/ro/docs/interaction-relations/" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: seeAlso ECO:0000353 +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "directly inhibits" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "directly activates" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: process_has_causal_agent ! process has causal agent + +[Typedef] +id: RO:0002501 +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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002506 +name: causal relation between entities +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 https://orcid.org/0000-0002-6601-2165 +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:0000002 ! continuant +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002566 +name: causally influences +def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002584 +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" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: has_part capable_of +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +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." [] +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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process + +[Typedef] +id: RO:0002596 +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." [] +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: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +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." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: capable_of negatively_regulates +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +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." [] +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: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 causally_upstream_of,_negative_effect +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: RO:0004050 RO:0002418 +is_a: causally_upstream_of_or_within ! causally upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: RO:0004049 RO:0002418 +is_a: causally_upstream_of_or_within ! causally upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: regulates ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + +[Typedef] +id: bearer_of +name: bearer of +name: has characteristic +namespace: external +def: "Inverse of characteristic_of" [] +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 ! specifically dependent continuant +is_inverse_functional: true + +[Typedef] +id: capable_of +name: capable of +namespace: external +namespace: uberon +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:0000117 https://orcid.org/0000-0002-6601-2165 +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 ! independent continuant +range: BFO:0000015 ! process +is_a: capable_of_part_of ! capable of part of + +[Typedef] +id: capable_of_part_of +name: capable of part of +namespace: external +namespace: uberon +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:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: causally_downstream_of +name: causally downstream of +namespace: external +def: "inverse of upstream of" [] +xref: RO:0002404 +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +namespace: external +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +xref: RO:0002427 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: causally_upstream_of +name: causally upstream of +namespace: external +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002411 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: precedes ! precedes + +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +namespace: external +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002305 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004050 RO:0002411 +is_a: causally_upstream_of ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +namespace: external +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] +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 +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002304 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004049 RO:0002411 +is_a: causally_upstream_of ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: causally_upstream_of_or_within +name: causally upstream of or within +namespace: external +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] +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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "influences (processual)" xsd:string +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: causally_downstream_of_or_within ! causally downstream of or within + +[Typedef] +id: dcterms-license +name: license +namespace: uberon +xref: http://purl.org/dc/terms/license +is_metadata_tag: true + +[Typedef] +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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: RO:0004050 RO:0002578 +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates + +[Typedef] +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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: RO:0004049 RO:0002578 +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates + +[Typedef] +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: RO:0002575 RO:0002211 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates + +[Typedef] +id: has_component +name: has component +namespace: external +namespace: uberon +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +xref: RO:0002180 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: has_input +name: has input +namespace: external +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002233 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "consumes" xsd:string +domain: BFO:0000015 ! process +is_a: has_participant ! has participant +inverse_of: input_of ! input of + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +namespace: external +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: has_part +name: has part +name: has_part +namespace: external +namespace: quality +namespace: uberon +def: "a core relation that holds between a whole and its part" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +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 +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] +id: has_quality +name: has quality +namespace: uberon +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: bearer_of ! bearer of + +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +namespace: external +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: regulated_by ! regulated by +is_a: RO:0002017 ! has component activity +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: immediately_causally_downstream_of +name: immediately causally downstream of +namespace: external +xref: RO:0002405 +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +namespace: external +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] +xref: RO:0002412 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +namespace: external +namespace: uberon +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 +namespace: external +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:0000117 https://orcid.org/0000-0002-7073-9172 +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: input_of +name: input of +namespace: uberon +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +xref: RO:0002352 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: participates_in ! participates in + +[Typedef] +id: negatively_regulated_by +name: negatively regulated by +namespace: external +def: "inverse of negatively regulates" [] +subset: RO:0002259 +xref: RO:0002335 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: regulated_by ! regulated by + +[Typedef] +id: negatively_regulates +name: negatively regulates +namespace: external +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002212 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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: RO:0004050 RO:0002211 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +is_a: regulates ! regulates +inverse_of: negatively_regulated_by ! negatively regulated by + +[Typedef] +id: negatively_regulates_characteristic +name: negatively regulates characteristic +namespace: gene_ontology +def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] +xref: RO:0019002 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: negatively_regulates positively_regulates_characteristic +holds_over_chain: positively_regulates negatively_regulates_characteristic +is_a: regulates_characteristic ! regulates characteristic + +[Typedef] +id: overlaps +name: overlaps +namespace: external +namespace: uberon +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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_symmetric: true +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: part_of +name: part of +name: part_of +namespace: external +namespace: quality +namespace: uberon +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +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 +is_transitive: true +is_a: overlaps ! overlaps +inverse_of: has_part ! has part + +[Typedef] +id: participates_in +name: participates in +namespace: external +namespace: uberon +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 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: has_participant ! has participant + +[Typedef] +id: positively_regulated_by +name: positively regulated by +namespace: external +def: "inverse of positively regulates" [] +subset: RO:0002259 +xref: RO:0002336 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: regulated_by ! regulated by + +[Typedef] +id: positively_regulates +name: positively regulates +namespace: external +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002213 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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: RO:0004049 RO:0002211 +holds_over_chain: negatively_regulates negatively_regulates +is_transitive: true +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +is_a: regulates ! regulates +inverse_of: positively_regulated_by ! positively regulated by + +[Typedef] +id: positively_regulates_characteristic +name: positively regulates characteristic +namespace: gene_ontology +def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] +xref: RO:0019001 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: positively_regulates positively_regulates_characteristic +is_a: regulates_characteristic ! regulates characteristic + +[Typedef] +id: preceded_by +name: preceded by +namespace: external +namespace: uberon +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 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of preceded_by +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: precedes ! precedes + +[Typedef] +id: precedes +name: precedes +namespace: external +namespace: uberon +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 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of precedes +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: process_has_causal_agent +name: process has causal agent +namespace: external +def: "Inverse of 'causal agent in process'" [] +xref: RO:0002608 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations + +[Typedef] +id: regulated_by +name: regulated by +namespace: external +def: "inverse of regulates" [] +subset: RO:0002259 +xref: RO:0002334 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000589 "regulated by (processual)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: causally_downstream_of_or_within ! causally downstream of or within + +[Typedef] +id: regulates +name: regulates +namespace: external +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002211 +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: directly_regulates directly_regulates +is_transitive: true +is_a: causally_upstream_of ! causally upstream of +inverse_of: regulated_by ! regulated by +transitive_over: RO:0002025 ! has effector activity + +[Typedef] +id: regulates_characteristic +name: regulates characteristic +namespace: gene_ontology +def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] +xref: RO:0019000 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +domain: BFO:0000015 ! process +range: PATO:0000001 ! quality +holds_over_chain: regulates regulates_characteristic + diff --git a/pko-full.owl b/pko-full.owl new file mode 100644 index 0000000..ad56279 --- /dev/null +++ b/pko-full.owl @@ -0,0 +1,4044 @@ + + + + + None + + pharmokinetic-ontology + 2023-09-03 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + http://purl.org/dc/terms/license + uberon + dcterms-license + true + dcterms-license + license + + + + + + + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + 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. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + BFO:0000050 + external + quality + uberon + part_of + + + + + part_of + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + 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. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + BFO:0000051 + external + quality + uberon + has_part + + + + has_part + has part + has part + has_part + + + + + + + + + + + + + + + + + preceded by + 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. + 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. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + BFO:0000062 + external + uberon + preceded_by + + preceded_by + preceded by + preceded by + + + + + + + + + + + + + + + + precedes + 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. + BFO:0000063 + external + uberon + precedes + + precedes + precedes + precedes + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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. + bearer_of + is bearer of + + RO:0000053 + external + bearer_of + bearer_of + bearer of + has characteristic + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + RO:0000056 + external + uberon + participates_in + participates_in + participates in + participates in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + 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. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + RO:0000057 + external + has_participant + has_participant + has participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + uberon + has_quality + has_quality + has quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + external + has_regulatory_component_activity + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + external + has_negative_regulatory_component_activity + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + RO:0002087 + external + uberon + immediately_preceded_by + immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + RO:0002090 + external + immediately_precedes + + immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + RO:0002131 + external + uberon + overlaps + + + + overlaps + overlaps + overlaps + + + + + + + + + true + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + RO:0002180 + external + uberon + has_component + + has_component + has component + has component + + + + + + + + + + + + + + + + + + + + + + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + + + + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + RO:0002211 + external + regulates + + + + regulates + regulates + regulates + + + + + + + + + + + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. + + + negatively regulates (process to process) + + RO:0002212 + external + negatively_regulates + + + + negatively_regulates + negatively regulates + negatively regulates + + + + + + + + + + + + + + + + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. + + + positively regulates (process to process) + + RO:0002213 + external + positively_regulates + + + + positively_regulates + positively regulates + positively regulates + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + 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. + + has function realized in + + + 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)". + RO:0002215 + external + uberon + capable_of + + capable_of + capable of + capable of + + + + + + + + + + + + + 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. + + has function in + RO:0002216 + external + uberon + capable_of_part_of + capable_of_part_of + capable of part of + capable of part of + + + + + + + + + + true + + + + + + + + + + + + + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + RO:0002233 + external + has_input + + + + + has_input + has input + has input + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + + + + + + + + + + + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + + + RO:0002304 + external + causally_upstream_of,_positive_effect + + + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + + + RO:0002305 + external + causally_upstream_of,_negative_effect + + + causally_upstream_of,_negative_effect + causally upstream of, negative effect + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. + + catalyzes + executes + has + is catalyzing + is executing + 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. + + enables + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + + actively involved in + enables part of + involved in + + + + + + + + + + inverse of enables + + + enabled by + + + + + + + + + + + + inverse of regulates + + regulated by (processual) + RO:0002334 + external + regulated_by + + regulated_by + regulated by + regulated by + + + + + + + + + inverse of negatively regulates + + RO:0002335 + external + negatively_regulated_by + + negatively_regulated_by + negatively regulated by + negatively regulated by + + + + + + + + + inverse of positively regulates + + RO:0002336 + external + positively_regulated_by + + positively_regulated_by + positively regulated by + positively regulated by + + + + + + + + + inverse of has input + + RO:0002352 + uberon + input_of + + + input_of + input of + input of + + + + + + + + + + + + inverse of upstream of + + RO:0002404 + external + causally_downstream_of + causally_downstream_of + causally downstream of + causally downstream of + + + + + + + + + + + + + RO:0002405 + external + immediately_causally_downstream_of + immediately_causally_downstream_of + immediately causally downstream of + immediately causally downstream of + + + + + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + + indirectly inhibits + + indirectly negatively regulates + + + + + + + + + + + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. + + RO:0002411 + external + causally_upstream_of + + + causally_upstream_of + causally upstream of + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. + + + RO:0002412 + external + immediately_causally_upstream_of + immediately_causally_upstream_of + immediately causally upstream of + immediately causally upstream of + + + + + + + + + + + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + + influences (processual) + RO:0002418 + external + affects + causally_upstream_of_or_within + causally_upstream_of_or_within + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + + + RO:0002427 + external + causally_downstream_of_or_within + + causally_downstream_of_or_within + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + + involved in negative regulation of + + + + + + + + + + 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 + OWL does not allow defining object properties via a Union + + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + 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. + Considering relabeling as 'pairwise interacts with' + + 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. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + + + molecularly controls + directly regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + + + directly inhibits + molecularly decreases activity of + directly negatively regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + + + directly activates + molecularly increases activity of + directly positively regulates activity of + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + + + 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 + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + + + + + + + + + + + + causally influenced by (entity-centric) + causally influenced by + + + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + + + + causally influences (entity-centric) + causally influences + + + + + + + + + + p directly regulates q iff p is immediately causally upstream of q and p regulates q. + + + directly regulates (processual) + + RO:0002578 + external + directly_regulates + + + + directly_regulates + directly regulates + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + 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 + + has part structure that is capable of + + + + + + + + + + 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. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + Inverse of 'causal agent in process' + + RO:0002608 + external + process_has_causal_agent + process_has_causal_agent + process has causal agent + + + + + + + + + + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. + + directly positively regulates (process to process) + + RO:0002629 + external + directly_positively_regulates + + + + directly_positively_regulates + directly positively regulates + + + + + + + + + + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. + + directly negatively regulates (process to process) + + RO:0002630 + external + directly_negatively_regulates + + + + directly_negatively_regulates + directly negatively regulates + + + + + + + + + + + + + + + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + + regulates activity of + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + RO:0019000 + gene_ontology + regulates_characteristic + regulates_characteristic + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + RO:0019001 + gene_ontology + positively_regulates_characteristic + positively_regulates_characteristic + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + RO:0019002 + gene_ontology + negatively_regulates_characteristic + negatively_regulates_characteristic + negatively regulates characteristic + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + A role is particular behaviour which a material entity may exhibit. + chebi_ontology + CHEBI:50906 + + role + + + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + GO:0005554 + molecular function + molecular_function + GO:0003674 + + + + + + + Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + molecular_function + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + GOC:pdt + + + + + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + Wikipedia:Enzyme + enzyme activity + molecular_function + GO:0003824 + + + + + + + + catalytic activity + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + GOC:vw + ISBN:0198506732 + + + + + enzyme activity + GOC:dph + GOC:tb + + + + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + https://github.com/geneontology/go-ontology/issues/24968 + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological_process + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + molecular_function + GO:0016301 + + + + + + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + Reactome:R-HSA-1483089 + Reactome:R-HSA-1483186 + Reactome:R-HSA-5668414 + Reactome:R-HSA-8868783 + molecular_function + GO:0016740 + + + + + + + + + + + transferase activity + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + ISBN:0198506732 + + + + + Reactome:R-HSA-1483089 + PE is converted to PS by PTDSS2 + + + + + Reactome:R-HSA-1483186 + PC is converted to PS by PTDSS1 + + + + + Reactome:R-HSA-5668414 + TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK + + + + + Reactome:R-HSA-8868783 + TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + EC:2.7.-.- + molecular_function + GO:0016772 + + Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. + transferase activity, transferring phosphorus-containing groups + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + GOC:jl + ISBN:0198506732 + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000072 + quality + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + root node + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/pko.obo b/pko.obo new file mode 100644 index 0000000..867a835 --- /dev/null +++ b/pko.obo @@ -0,0 +1,1375 @@ +format-version: 1.2 +data-version: http://si.eu-parc.eu/pko/releases/2023-09-03/pko.owl +subsetdef: 3_STAR "" +subsetdef: goslim_agr "" +subsetdef: goslim_candida "" +subsetdef: goslim_chembl "" +subsetdef: goslim_drosophila "" +subsetdef: goslim_flybase_ribbon "" +subsetdef: goslim_generic "" +subsetdef: goslim_metagenomics "" +subsetdef: goslim_mouse "" +subsetdef: goslim_pir "" +subsetdef: goslim_plant "" +subsetdef: goslim_pombe "" +subsetdef: goslim_yeast "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: prokaryote_subset "" +subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +ontology: http://si.eu-parc.eu/pko.owl +property_value: dcterms-license https://creativecommons.org/licenses/unspecified +property_value: http://purl.org/dc/terms/description "None" xsd:string +property_value: http://purl.org/dc/terms/title "pharmokinetic-ontology" xsd:string +property_value: owl:versionInfo "2023-09-03" xsd:string + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +relationship: part_of BFO:0000002 {all_only="true"} ! continuant + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: part_of BFO:0000003 {all_only="true"} ! occurrent + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: part_of BFO:0000019 {all_only="true"} ! quality + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: CHEBI:50906 ! role +equivalent_to: CHEBI:50906 ! role + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CHEBI:50906 +name: role +namespace: chebi_ontology +def: "A role is particular behaviour which a material entity may exhibit." [] +subset: 3_STAR +is_a: BFO:0000023 ! role + +[Term] +id: GO:0003674 +name: molecular_function +namespace: molecular_function +alt_id: GO:0005554 +def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] +comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +subset: goslim_candida +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process + +[Term] +id: GO:0003824 +name: catalytic activity +namespace: molecular_function +def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] +subset: goslim_agr +subset: goslim_chembl +subset: goslim_flybase_ribbon +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] +xref: Wikipedia:Enzyme +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. +subset: goslim_candida +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI +created_by: jl +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0016301 +name: kinase activity +namespace: molecular_function +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +synonym: "phosphokinase activity" EXACT [] +xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" +xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups + +[Term] +id: GO:0016740 +name: transferase activity +namespace: molecular_function +def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_mouse +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: prokaryote_subset +xref: EC:2.-.-.- +xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" +xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" +xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK" +xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248" +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +namespace: molecular_function +def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] +comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. +subset: goslim_chembl +xref: EC:2.7.-.- +is_a: GO:0016740 ! transferase activity + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: PKO:0000000 +name: root node + +[Typedef] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +inverse_of: bearer_of ! bearer of + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: has_quality ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: bearer_of ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: bearer_of ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: bearer_of ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +is_a: RO:0000052 ! characteristic of + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +is_a: regulated_by ! regulated by +inverse_of: directly_regulates ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: directly_negatively_regulates ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: directly_positively_regulates ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +is_functional: true +is_a: RO:0002017 ! has component activity +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002222 +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 +property_value: http://purl.org/dc/terms/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 https://orcid.org/0000-0002-6601-2165 +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 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 causally_upstream_of +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 causally_upstream_of_or_within +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002327 +name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +is_a: capable_of ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: has_part ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 part_of +is_a: participates_in ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: has_participant ! has participant + +[Typedef] +id: RO:0002407 +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +holds_over_chain: directly_positively_regulates directly_positively_regulates +holds_over_chain: directly_positively_regulates RO:0002407 +holds_over_chain: RO:0002409 RO:0002409 +is_transitive: true +is_a: positively_regulates ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: directly_positively_regulates ! directly positively regulates + +[Typedef] +id: RO:0002409 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: directly_negatively_regulates directly_negatively_regulates +holds_over_chain: directly_negatively_regulates RO:0002409 +is_transitive: true +is_a: negatively_regulates ! negatively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: directly_negatively_regulates ! directly negatively regulates + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002327 regulates +holds_over_chain: RO:0002331 regulates +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 positively_regulates +holds_over_chain: RO:0002331 positively_regulates +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 negatively_regulates +holds_over_chain: RO:0002331 negatively_regulates +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +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" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002434 +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 [] +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" 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 https://orcid.org/0000-0002-6601-2165 +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/ro/docs/interaction-relations/" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: seeAlso ECO:0000353 +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "directly inhibits" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "directly activates" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: process_has_causal_agent ! process has causal agent + +[Typedef] +id: RO:0002501 +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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002506 +name: causal relation between entities +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 https://orcid.org/0000-0002-6601-2165 +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:0000002 ! continuant +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002566 +name: causally influences +def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002584 +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" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: has_part capable_of +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +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." [] +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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process + +[Typedef] +id: RO:0002596 +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." [] +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: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +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." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: capable_of negatively_regulates +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +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." [] +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: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 causally_upstream_of,_negative_effect +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: RO:0004050 RO:0002418 +is_a: causally_upstream_of_or_within ! causally upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: RO:0004049 RO:0002418 +is_a: causally_upstream_of_or_within ! causally upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: causally_upstream_of ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: regulates ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + +[Typedef] +id: bearer_of +name: bearer of +name: has characteristic +namespace: external +def: "Inverse of characteristic_of" [] +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 ! specifically dependent continuant +is_inverse_functional: true + +[Typedef] +id: capable_of +name: capable of +namespace: external +namespace: uberon +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:0000117 https://orcid.org/0000-0002-6601-2165 +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 ! independent continuant +range: BFO:0000015 ! process +is_a: capable_of_part_of ! capable of part of + +[Typedef] +id: capable_of_part_of +name: capable of part of +namespace: external +namespace: uberon +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:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: causally_downstream_of +name: causally downstream of +namespace: external +def: "inverse of upstream of" [] +xref: RO:0002404 +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +namespace: external +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +xref: RO:0002427 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: causally_upstream_of +name: causally upstream of +namespace: external +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002411 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: causally_upstream_of_or_within ! causally upstream of or within +is_a: precedes ! precedes + +[Typedef] +id: causally_upstream_of,_negative_effect +name: causally upstream of, negative effect +namespace: external +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002305 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004050 RO:0002411 +is_a: causally_upstream_of ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: causally_upstream_of,_positive_effect +name: causally upstream of, positive effect +namespace: external +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] +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 +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002304 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004049 RO:0002411 +is_a: causally_upstream_of ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: causally_upstream_of_or_within +name: causally upstream of or within +namespace: external +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] +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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "influences (processual)" xsd:string +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: causally_downstream_of_or_within ! causally downstream of or within + +[Typedef] +id: dcterms-license +name: license +namespace: uberon +xref: http://purl.org/dc/terms/license +is_metadata_tag: true + +[Typedef] +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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: RO:0004050 RO:0002578 +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates + +[Typedef] +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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: RO:0004049 RO:0002578 +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates + +[Typedef] +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: RO:0002575 RO:0002211 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates + +[Typedef] +id: has_component +name: has component +namespace: external +namespace: uberon +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +xref: RO:0002180 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: has_input +name: has input +namespace: external +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002233 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "consumes" xsd:string +domain: BFO:0000015 ! process +is_a: has_participant ! has participant +inverse_of: input_of ! input of + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +namespace: external +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: has_part +name: has part +name: has_part +namespace: external +namespace: quality +namespace: uberon +def: "a core relation that holds between a whole and its part" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +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 +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] +id: has_quality +name: has quality +namespace: uberon +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: bearer_of ! bearer of + +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +namespace: external +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: regulated_by ! regulated by +is_a: RO:0002017 ! has component activity +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: immediately_causally_downstream_of +name: immediately causally downstream of +namespace: external +xref: RO:0002405 +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +namespace: external +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] +xref: RO:0002412 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +namespace: external +namespace: uberon +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 +namespace: external +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:0000117 https://orcid.org/0000-0002-7073-9172 +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: input_of +name: input of +namespace: uberon +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +xref: RO:0002352 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: participates_in ! participates in + +[Typedef] +id: negatively_regulated_by +name: negatively regulated by +namespace: external +def: "inverse of negatively regulates" [] +subset: RO:0002259 +xref: RO:0002335 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: regulated_by ! regulated by + +[Typedef] +id: negatively_regulates +name: negatively regulates +namespace: external +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002212 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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: RO:0004050 RO:0002211 +is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect +is_a: regulates ! regulates +inverse_of: negatively_regulated_by ! negatively regulated by + +[Typedef] +id: negatively_regulates_characteristic +name: negatively regulates characteristic +namespace: gene_ontology +def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] +xref: RO:0019002 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: negatively_regulates positively_regulates_characteristic +holds_over_chain: positively_regulates negatively_regulates_characteristic +is_a: regulates_characteristic ! regulates characteristic + +[Typedef] +id: overlaps +name: overlaps +namespace: external +namespace: uberon +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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_symmetric: true +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: part_of +name: part of +name: part_of +namespace: external +namespace: quality +namespace: uberon +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +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 +is_transitive: true +is_a: overlaps ! overlaps +inverse_of: has_part ! has part + +[Typedef] +id: participates_in +name: participates in +namespace: external +namespace: uberon +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 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: has_participant ! has participant + +[Typedef] +id: positively_regulated_by +name: positively regulated by +namespace: external +def: "inverse of positively regulates" [] +subset: RO:0002259 +xref: RO:0002336 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: regulated_by ! regulated by + +[Typedef] +id: positively_regulates +name: positively regulates +namespace: external +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002213 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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: RO:0004049 RO:0002211 +holds_over_chain: negatively_regulates negatively_regulates +is_transitive: true +is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect +is_a: regulates ! regulates +inverse_of: positively_regulated_by ! positively regulated by + +[Typedef] +id: positively_regulates_characteristic +name: positively regulates characteristic +namespace: gene_ontology +def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] +xref: RO:0019001 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: positively_regulates positively_regulates_characteristic +is_a: regulates_characteristic ! regulates characteristic + +[Typedef] +id: preceded_by +name: preceded by +namespace: external +namespace: uberon +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 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of preceded_by +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: precedes ! precedes + +[Typedef] +id: precedes +name: precedes +namespace: external +namespace: uberon +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 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of precedes +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: process_has_causal_agent +name: process has causal agent +namespace: external +def: "Inverse of 'causal agent in process'" [] +xref: RO:0002608 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations + +[Typedef] +id: regulated_by +name: regulated by +namespace: external +def: "inverse of regulates" [] +subset: RO:0002259 +xref: RO:0002334 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000589 "regulated by (processual)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: causally_downstream_of_or_within ! causally downstream of or within + +[Typedef] +id: regulates +name: regulates +namespace: external +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002211 +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +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 +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: directly_regulates directly_regulates +is_transitive: true +is_a: causally_upstream_of ! causally upstream of +inverse_of: regulated_by ! regulated by +transitive_over: RO:0002025 ! has effector activity + +[Typedef] +id: regulates_characteristic +name: regulates characteristic +namespace: gene_ontology +def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] +xref: RO:0019000 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +domain: BFO:0000015 ! process +range: PATO:0000001 ! quality +holds_over_chain: regulates regulates_characteristic + diff --git a/pko.owl b/pko.owl new file mode 100644 index 0000000..5865650 --- /dev/null +++ b/pko.owl @@ -0,0 +1,4044 @@ + + + + + None + + pharmokinetic-ontology + 2023-09-03 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + http://purl.org/dc/terms/license + uberon + dcterms-license + true + dcterms-license + license + + + + + + + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + 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. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + BFO:0000050 + external + quality + uberon + part_of + + + + + part_of + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + 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. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + BFO:0000051 + external + quality + uberon + has_part + + + + has_part + has part + has part + has_part + + + + + + + + + + + + + + + + + preceded by + 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. + 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. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + BFO:0000062 + external + uberon + preceded_by + + preceded_by + preceded by + preceded by + + + + + + + + + + + + + + + + precedes + 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. + BFO:0000063 + external + uberon + precedes + + precedes + precedes + precedes + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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. + bearer_of + is bearer of + + RO:0000053 + external + bearer_of + bearer_of + bearer of + has characteristic + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + RO:0000056 + external + uberon + participates_in + participates_in + participates in + participates in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + 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. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + RO:0000057 + external + has_participant + has_participant + has participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + uberon + has_quality + has_quality + has quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + external + has_regulatory_component_activity + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + external + has_negative_regulatory_component_activity + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + RO:0002087 + external + uberon + immediately_preceded_by + immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + RO:0002090 + external + immediately_precedes + + immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + RO:0002131 + external + uberon + overlaps + + + + overlaps + overlaps + overlaps + + + + + + + + + true + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + RO:0002180 + external + uberon + has_component + + has_component + has component + has component + + + + + + + + + + + + + + + + + + + + + + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + + + + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + RO:0002211 + external + regulates + + + + regulates + regulates + regulates + + + + + + + + + + + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. + + + negatively regulates (process to process) + + RO:0002212 + external + negatively_regulates + + + + negatively_regulates + negatively regulates + negatively regulates + + + + + + + + + + + + + + + + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. + + + positively regulates (process to process) + + RO:0002213 + external + positively_regulates + + + + positively_regulates + positively regulates + positively regulates + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + 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. + + has function realized in + + + 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)". + RO:0002215 + external + uberon + capable_of + + capable_of + capable of + capable of + + + + + + + + + + + + + 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. + + has function in + RO:0002216 + external + uberon + capable_of_part_of + capable_of_part_of + capable of part of + capable of part of + + + + + + + + + + true + + + + + + + + + + + + + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + RO:0002233 + external + has_input + + + + + has_input + has input + has input + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + + + + + + + + + + + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + + + RO:0002304 + external + causally_upstream_of,_positive_effect + + + causally_upstream_of,_positive_effect + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + + + RO:0002305 + external + causally_upstream_of,_negative_effect + + + causally_upstream_of,_negative_effect + causally upstream of, negative effect + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. + + catalyzes + executes + has + is catalyzing + is executing + 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. + + enables + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + + actively involved in + enables part of + involved in + + + + + + + + + + inverse of enables + + + enabled by + + + + + + + + + + + + inverse of regulates + + regulated by (processual) + RO:0002334 + external + regulated_by + + regulated_by + regulated by + regulated by + + + + + + + + + inverse of negatively regulates + + RO:0002335 + external + negatively_regulated_by + + negatively_regulated_by + negatively regulated by + negatively regulated by + + + + + + + + + inverse of positively regulates + + RO:0002336 + external + positively_regulated_by + + positively_regulated_by + positively regulated by + positively regulated by + + + + + + + + + inverse of has input + + RO:0002352 + uberon + input_of + + + input_of + input of + input of + + + + + + + + + + + + inverse of upstream of + + RO:0002404 + external + causally_downstream_of + causally_downstream_of + causally downstream of + causally downstream of + + + + + + + + + + + + + RO:0002405 + external + immediately_causally_downstream_of + immediately_causally_downstream_of + immediately causally downstream of + immediately causally downstream of + + + + + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + + indirectly inhibits + + indirectly negatively regulates + + + + + + + + + + + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. + + RO:0002411 + external + causally_upstream_of + + + causally_upstream_of + causally upstream of + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. + + + RO:0002412 + external + immediately_causally_upstream_of + immediately_causally_upstream_of + immediately causally upstream of + immediately causally upstream of + + + + + + + + + + + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + + influences (processual) + RO:0002418 + external + affects + causally_upstream_of_or_within + causally_upstream_of_or_within + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + + + RO:0002427 + external + causally_downstream_of_or_within + + causally_downstream_of_or_within + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + + involved in negative regulation of + + + + + + + + + + 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 + OWL does not allow defining object properties via a Union + + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + 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. + Considering relabeling as 'pairwise interacts with' + + 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. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + + + molecularly controls + directly regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + + + directly inhibits + molecularly decreases activity of + directly negatively regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + + + directly activates + molecularly increases activity of + directly positively regulates activity of + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + + + 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 + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + + + + + + + + + + + + causally influenced by (entity-centric) + causally influenced by + + + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + + + + causally influences (entity-centric) + causally influences + + + + + + + + + + p directly regulates q iff p is immediately causally upstream of q and p regulates q. + + + directly regulates (processual) + + RO:0002578 + external + directly_regulates + + + + directly_regulates + directly regulates + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + 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 + + has part structure that is capable of + + + + + + + + + + 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. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + Inverse of 'causal agent in process' + + RO:0002608 + external + process_has_causal_agent + process_has_causal_agent + process has causal agent + + + + + + + + + + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. + + directly positively regulates (process to process) + + RO:0002629 + external + directly_positively_regulates + + + + directly_positively_regulates + directly positively regulates + + + + + + + + + + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. + + directly negatively regulates (process to process) + + RO:0002630 + external + directly_negatively_regulates + + + + directly_negatively_regulates + directly negatively regulates + + + + + + + + + + + + + + + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + + regulates activity of + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + RO:0019000 + gene_ontology + regulates_characteristic + regulates_characteristic + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + RO:0019001 + gene_ontology + positively_regulates_characteristic + positively_regulates_characteristic + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + RO:0019002 + gene_ontology + negatively_regulates_characteristic + negatively_regulates_characteristic + negatively regulates characteristic + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + A role is particular behaviour which a material entity may exhibit. + chebi_ontology + CHEBI:50906 + + role + + + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + GO:0005554 + molecular function + molecular_function + GO:0003674 + + + + + + + Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + molecular_function + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + GOC:pdt + + + + + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + Wikipedia:Enzyme + enzyme activity + molecular_function + GO:0003824 + + + + + + + + catalytic activity + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + GOC:vw + ISBN:0198506732 + + + + + enzyme activity + GOC:dph + GOC:tb + + + + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + https://github.com/geneontology/go-ontology/issues/24968 + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological_process + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + molecular_function + GO:0016301 + + + + + + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + Reactome:R-HSA-1483089 + Reactome:R-HSA-1483186 + Reactome:R-HSA-5668414 + Reactome:R-HSA-8868783 + molecular_function + GO:0016740 + + + + + + + + + + + transferase activity + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + ISBN:0198506732 + + + + + Reactome:R-HSA-1483089 + PE is converted to PS by PTDSS2 + + + + + Reactome:R-HSA-1483186 + PC is converted to PS by PTDSS1 + + + + + Reactome:R-HSA-5668414 + TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK + + + + + Reactome:R-HSA-8868783 + TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + EC:2.7.-.- + molecular_function + GO:0016772 + + Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. + transferase activity, transferring phosphorus-containing groups + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + GOC:jl + ISBN:0198506732 + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000072 + quality + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + root node + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +