diff --git a/fbdv-base.json b/fbdv-base.json index 1e45180..970ee2d 100644 --- a/fbdv-base.json +++ b/fbdv-base.json @@ -3218,7 +3218,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "06:12:2021 09:25" + "val": "24:01:2022 09:24" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -3230,11 +3230,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-12-06" + "val": "2022-01-24" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-12-06/fbdv-base.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-01-24/fbdv-base.json", "xrefs": [] }, "nodes": [ diff --git a/fbdv-base.obo b/fbdv-base.obo index 8ac72b0..88ee6f3 100644 --- a/fbdv-base.obo +++ b/fbdv-base.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-12-06/fbdv-base.owl -date: 06:12:2021 09:25 +data-version: fbdv/releases/2022-01-24/fbdv-base.owl +date: 24:01:2022 09:24 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" @@ -30,7 +30,7 @@ property_value: IAO:0000700 FBdv:00000000 property_value: IAO:0000700 FBdv:00005259 property_value: IAO:0000700 FBdv:00007013 property_value: IAO:0000700 FBdv:00007024 -property_value: owl:versionInfo "2021-12-06" xsd:string +property_value: owl:versionInfo "2022-01-24" xsd:string [Term] id: FBdv:00000000 diff --git a/fbdv-base.owl b/fbdv-base.owl index c04e791..1e68dd3 100644 --- a/fbdv-base.owl +++ b/fbdv-base.owl @@ -12,7 +12,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -26,10 +26,10 @@ https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 06:12:2021 09:25 + 24:01:2022 09:24 FlyBase_development_CV 1.2 - 2021-12-06 + 2022-01-24 diff --git a/fbdv-full.json b/fbdv-full.json index 2ab0d8c..ba6e091 100644 --- a/fbdv-full.json +++ b/fbdv-full.json @@ -220,6 +220,15 @@ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, + { + "domainClassIds": [ + "http://purl.obolibrary.org/obo/BFO_0000015" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019000", + "rangeClassIds": [ + "http://purl.obolibrary.org/obo/PATO_0000001" + ] + }, { "domainClassIds": [ "http://purl.obolibrary.org/obo/BFO_0000040" @@ -386,6 +395,11 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/BFO_0000019" }, + { + "obj": "http://purl.obolibrary.org/obo/BFO_0000020", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/PATO_0000001" + }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000050", "pred": "subPropertyOf", @@ -4251,6 +4265,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002608" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002410", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0019000" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002411", "pred": "inverseOf", @@ -4510,6 +4529,16 @@ "obj": "http://purl.obolibrary.org/obo/RO_0011002", "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002448" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0019000", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0019001" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0019000", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0019002" } ], "equivalentNodesSets": [], @@ -4676,7 +4705,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "06:12:2021 09:24" + "val": "24:01:2022 09:23" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -4688,11 +4717,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-12-06" + "val": "2022-01-24" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-12-06/fbdv-full.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-01-24/fbdv-full.json", "xrefs": [] }, "nodes": [ @@ -10660,7 +10689,6 @@ "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", @@ -11416,6 +11444,19 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/PATO_0000001", + "lbl": "quality", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000589", + "val": "quality (PATO)" + } + ] + }, + "type": "CLASS" + }, { "id": "http://purl.obolibrary.org/obo/RO_0000052", "lbl": "characteristic of", @@ -11768,7 +11809,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002012", - "lbl": "occurent part of", + "lbl": "occurent_part_of", "meta": { "basicPropertyValues": [ { @@ -11781,7 +11822,7 @@ } ], "definition": { - "val": "A part of relation that applies only between occurents.", + "val": "A part of relation that applies only between occurrents.", "xrefs": [] }, "xrefs": [ @@ -12956,10 +12997,6 @@ { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." } ], "subsets": [ @@ -14310,6 +14347,94 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/RO_0017001", + "lbl": "utilizes", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "A diagnostic testing device utilizes a specimen." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Asiyah Lin" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "https://orcid.org/0000-0001-9625-1899 Bill Duncan" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-08" + } + ], + "definition": { + "val": "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0019000", + "lbl": "regulates characteristic", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0002-8688-6599" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0019001", + "lbl": "positively regulates characteristic", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0002-8688-6599" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0019002", + "lbl": "negatively regulates characteristic", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0002-8688-6599" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/fbdv#systematic_synonym", "lbl": "Systematic synonym", @@ -14712,6 +14837,13 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002428" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002211", + "http://purl.obolibrary.org/obo/RO_0019000" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019000" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002212", @@ -14740,6 +14872,13 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002430" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002212", + "http://purl.obolibrary.org/obo/RO_0019001" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019002" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002213", @@ -14761,6 +14900,27 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002429" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002213", + "http://purl.obolibrary.org/obo/RO_0019001" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019001" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002213", + "http://purl.obolibrary.org/obo/RO_0019002" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019002" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002215", + "http://purl.obolibrary.org/obo/RO_0002233" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0017001" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002233", diff --git a/fbdv-full.obo b/fbdv-full.obo index 888b7c5..bed35ef 100644 --- a/fbdv-full.obo +++ b/fbdv-full.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-12-06/fbdv-full.owl -date: 06:12:2021 09:24 +data-version: fbdv/releases/2022-01-24/fbdv-full.owl +date: 24:01:2022 09:23 subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "" @@ -50,7 +50,7 @@ property_value: IAO:0000700 FBdv:00000000 property_value: IAO:0000700 FBdv:00005259 property_value: IAO:0000700 FBdv:00007013 property_value: IAO:0000700 FBdv:00007024 -property_value: owl:versionInfo "2021-12-06" xsd:string +property_value: owl:versionInfo "2022-01-24" xsd:string [Term] id: BFO:0000002 @@ -2235,7 +2235,6 @@ comment: Note that, in addition to forming the root of the biological process on subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl -subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant @@ -2496,6 +2495,12 @@ relationship: part_of GO:0000278 ! mitotic cell cycle created_by: jl creation_date: 2014-05-22T14:22:34Z +[Term] +id: PATO:0000001 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string + [Typedef] id: BFO:0000062 name: preceded by @@ -3112,7 +3117,6 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string -property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part @@ -3671,6 +3675,45 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences +[Typedef] +id: RO:0017001 +name: utilizes +def: "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y." [] +property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string +property_value: IAO:0000117 "Asiyah Lin" xsd:string +property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899 Bill Duncan" xsd:string +property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string +property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string +holds_over_chain: RO:0002215 RO:0002233 +creation_date: 2021-11-08 + +[Typedef] +id: RO:0019000 +name: regulates characteristic +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." [] +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: RO:0002211 RO:0019000 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0019001 +name: positively regulates characteristic +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." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: RO:0002213 RO:0019001 +is_a: RO:0019000 ! regulates characteristic + +[Typedef] +id: RO:0019002 +name: negatively regulates characteristic +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." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: RO:0002212 RO:0019001 +holds_over_chain: RO:0002213 RO:0019002 +is_a: RO:0019000 ! regulates characteristic + [Typedef] id: ends_during name: ends_during @@ -3733,8 +3776,8 @@ inverse_of: RO:0002090 ! immediately precedes [Typedef] id: occurent_part_of -name: occurent_part_of -def: "A part of relation that applies only between occurents." [] +name: occurrent part of +def: "A part of relation that applies only between occurrents." [] xref: RO:0002012 domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent @@ -3782,5 +3825,5 @@ comment: Creating this relation as a temporary fix, pending adding the axiom occ xref: FBdv:00018001 is_transitive: true is_a: happens_during ! happens during -is_a: occurent_part_of ! occurent part of +is_a: occurent_part_of ! occurrent part of diff --git a/fbdv-full.owl b/fbdv-full.owl index dae48c4..f52aba3 100644 --- a/fbdv-full.owl +++ b/fbdv-full.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -31,10 +31,10 @@ FlyBase Developmental Ontology (FBdv) https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 06:12:2021 09:24 + 24:01:2022 09:23 FlyBase_development_CV 1.2 - 2021-12-06 + 2022-01-24 @@ -508,6 +508,12 @@ + + + + + + @@ -1038,13 +1044,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. + A part of relation that applies only between occurrents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of - occurent part of occurent_part_of + occurrent part of @@ -1805,7 +1811,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables @@ -2695,6 +2700,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + 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. + + 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. + + 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. + + negatively regulates characteristic + + + + + + + + quality (PATO) + quality + + + + + + + + + @@ -1038,13 +1044,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. + A part of relation that applies only between occurrents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of - occurent part of occurent_part_of + occurrent part of @@ -1805,7 +1811,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables @@ -2695,6 +2700,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + 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. + + 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. + + 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. + + negatively regulates characteristic + + + + + + + + quality (PATO) + quality + + + + - A part of relation that applies only between occurents. + A part of relation that applies only between occurrents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of - occurent part of occurent_part_of + occurrent part of diff --git a/fbdv.json b/fbdv.json index 514bc23..b532087 100644 --- a/fbdv.json +++ b/fbdv.json @@ -220,6 +220,15 @@ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, + { + "domainClassIds": [ + "http://purl.obolibrary.org/obo/BFO_0000015" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019000", + "rangeClassIds": [ + "http://purl.obolibrary.org/obo/PATO_0000001" + ] + }, { "domainClassIds": [ "http://purl.obolibrary.org/obo/BFO_0000040" @@ -386,6 +395,11 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/BFO_0000019" }, + { + "obj": "http://purl.obolibrary.org/obo/BFO_0000020", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/PATO_0000001" + }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000050", "pred": "subPropertyOf", @@ -4251,6 +4265,11 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002608" }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0002410", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0019000" + }, { "obj": "http://purl.obolibrary.org/obo/RO_0002411", "pred": "inverseOf", @@ -4510,6 +4529,16 @@ "obj": "http://purl.obolibrary.org/obo/RO_0011002", "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002448" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0019000", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0019001" + }, + { + "obj": "http://purl.obolibrary.org/obo/RO_0019000", + "pred": "subPropertyOf", + "sub": "http://purl.obolibrary.org/obo/RO_0019002" } ], "equivalentNodesSets": [], @@ -4676,7 +4705,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "06:12:2021 09:24" + "val": "24:01:2022 09:23" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -4688,11 +4717,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-12-06" + "val": "2022-01-24" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-12-06/fbdv.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-01-24/fbdv.json", "xrefs": [] }, "nodes": [ @@ -10660,7 +10689,6 @@ "http://purl.obolibrary.org/obo/go#goslim_aspergillus", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", @@ -11416,6 +11444,19 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/PATO_0000001", + "lbl": "quality", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000589", + "val": "quality (PATO)" + } + ] + }, + "type": "CLASS" + }, { "id": "http://purl.obolibrary.org/obo/RO_0000052", "lbl": "characteristic of", @@ -11768,7 +11809,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002012", - "lbl": "occurent part of", + "lbl": "occurent_part_of", "meta": { "basicPropertyValues": [ { @@ -11781,7 +11822,7 @@ } ], "definition": { - "val": "A part of relation that applies only between occurents.", + "val": "A part of relation that applies only between occurrents.", "xrefs": [] }, "xrefs": [ @@ -12956,10 +12997,6 @@ { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." } ], "subsets": [ @@ -14310,6 +14347,94 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/RO_0017001", + "lbl": "utilizes", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "A diagnostic testing device utilizes a specimen." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Asiyah Lin" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "https://orcid.org/0000-0001-9625-1899 Bill Duncan" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-08" + } + ], + "definition": { + "val": "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0019000", + "lbl": "regulates characteristic", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0002-8688-6599" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0019001", + "lbl": "positively regulates characteristic", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0002-8688-6599" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/RO_0019002", + "lbl": "negatively regulates characteristic", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.org/dc/terms/contributor", + "val": "https://orcid.org/0000-0002-8688-6599" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/fbdv#systematic_synonym", "lbl": "Systematic synonym", @@ -14712,6 +14837,13 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002428" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002211", + "http://purl.obolibrary.org/obo/RO_0019000" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019000" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002212", @@ -14740,6 +14872,13 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002430" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002212", + "http://purl.obolibrary.org/obo/RO_0019001" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019002" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002213", @@ -14761,6 +14900,27 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002429" }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002213", + "http://purl.obolibrary.org/obo/RO_0019001" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019001" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002213", + "http://purl.obolibrary.org/obo/RO_0019002" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0019002" + }, + { + "chainPredicateIds": [ + "http://purl.obolibrary.org/obo/RO_0002215", + "http://purl.obolibrary.org/obo/RO_0002233" + ], + "predicateId": "http://purl.obolibrary.org/obo/RO_0017001" + }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002233", diff --git a/fbdv.obo b/fbdv.obo index 5d749d6..aaa6381 100644 --- a/fbdv.obo +++ b/fbdv.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-12-06 -date: 06:12:2021 09:24 +data-version: fbdv/releases/2022-01-24 +date: 24:01:2022 09:23 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" @@ -33,7 +33,7 @@ property_value: IAO:0000700 FBdv:00000000 property_value: IAO:0000700 FBdv:00005259 property_value: IAO:0000700 FBdv:00007013 property_value: IAO:0000700 FBdv:00007024 -property_value: owl:versionInfo "2021-12-06" xsd:string +property_value: owl:versionInfo "2022-01-24" xsd:string [Term] id: FBdv:00000000 @@ -2027,8 +2027,8 @@ property_value: IAO:0000118 "starts_at_end_of" xsd:string [Typedef] id: occurent_part_of -name: occurent_part_of -def: "A part of relation that applies only between occurents." [] +name: occurrent part of +def: "A part of relation that applies only between occurrents." [] xref: RO:0002012 [Typedef] @@ -2039,5 +2039,5 @@ comment: Creating this relation as a temporary fix, pending adding the axiom occ xref: FBdv:00018001 is_transitive: true is_a: happens_during ! happens during -is_a: occurent_part_of ! occurent part of +is_a: occurent_part_of ! occurrent part of diff --git a/fbdv.owl b/fbdv.owl index 2872f10..838b528 100644 --- a/fbdv.owl +++ b/fbdv.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -31,10 +31,10 @@ FlyBase Developmental Ontology (FBdv) https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 06:12:2021 09:24 + 24:01:2022 09:23 FlyBase_development_CV 1.2 - 2021-12-06 + 2022-01-24 @@ -508,6 +508,12 @@ + + + + + + @@ -1038,13 +1044,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. + A part of relation that applies only between occurrents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of - occurent part of occurent_part_of + occurrent part of @@ -1805,7 +1811,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables @@ -2695,6 +2700,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + 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. + + 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. + + 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. + + negatively regulates characteristic + + + + + + + + quality (PATO) + quality + + + + + + + + + @@ -678,8 +684,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. - occurent part of + A part of relation that applies only between occurrents. + occurrent part of @@ -1425,7 +1431,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables @@ -2315,6 +2320,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + 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. + + 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. + + 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. + + negatively regulates characteristic + + + + + + + + quality (PATO) + quality + + + + + + + + + @@ -1038,13 +1044,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. + A part of relation that applies only between occurrents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of - occurent part of occurent_part_of + occurrent part of @@ -1805,7 +1811,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables @@ -2695,6 +2700,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + 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. + + 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. + + 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. + + negatively regulates characteristic + + + + + + + + quality (PATO) + quality + + + + + + + + + @@ -678,8 +684,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. - occurent part of + A part of relation that applies only between occurrents. + occurrent part of @@ -1425,7 +1431,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables @@ -2315,6 +2320,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + 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. + + 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. + + 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. + + negatively regulates characteristic + + + + + + + + quality (PATO) + quality + + + +