From ce5df6a1d15b3a75065b231dfb31dde4c6420ee3 Mon Sep 17 00:00:00 2001 From: Andy Deans Date: Fri, 19 Apr 2024 09:57:54 -0400 Subject: [PATCH] lots of updates added description, updated pages, some new classes --- gallont-base.json | 182 +++- gallont-base.obo | 69 +- gallont-base.owl | 188 +++- gallont-full.json | 441 +++++++- gallont-full.obo | 164 ++- gallont-full.owl | 1332 +++++++------------------ gallont.json | 441 +++++++- gallont.obo | 164 ++- gallont.owl | 1384 ++++++++------------------ src/ontology/imports/bfo_import.owl | 4 +- src/ontology/imports/pato_import.owl | 4 +- src/ontology/imports/po_import.owl | 171 +++- src/ontology/imports/ro_import.owl | 14 +- 13 files changed, 2403 insertions(+), 2155 deletions(-) diff --git a/gallont-base.json b/gallont-base.json index ed161a7..f51ebb6 100644 --- a/gallont-base.json +++ b/gallont-base.json @@ -7,7 +7,7 @@ "val" : "http://purl.obolibrary.org/obo/IAO_8000001" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "None" + "val" : "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" @@ -16,9 +16,9 @@ "val" : "Plant Gall Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-08" + "val" : "2024-04-19" } ], - "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-04-08/gallont-base.json" + "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-04-19/gallont-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000000", @@ -933,6 +933,131 @@ "val" : "2023-08-01T21:56:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "lbl" : "plant gall cluster", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-11T14:32:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "lbl" : "zoocecidium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A plant gall that is induced by an animal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-15T13:33:50Z" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://doi.org/10.1007/978-94-017-6230-4_9" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000051", + "lbl" : "plant gall abscission zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abscission zone (PO:0000146) that is part of a plant gall." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/129032167" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-18T13:34:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000052", + "lbl" : "hasDiameterInMm", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-27T01:25:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000053", + "lbl" : "plant gall dehiscence zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/179039203" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-18T14:16:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "lbl" : "induced by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000041", + "lbl" : "hasLengthInMm", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "For use with integral galls" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-11T14:02:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000060", + "lbl" : "hasHeightInMm", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-27T17:30:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000062", + "lbl" : "has seasonal maturity", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000150", + "lbl" : "has seasonal emergence", + "type" : "PROPERTY" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000002", @@ -1185,15 +1310,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000047", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", "pred" : "is_a", @@ -1204,8 +1325,40 @@ "obj" : "http://purl.obolibrary.org/obo/PO_0006504" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", - "pred" : "http://purl.obolibrary.org/obo/RO_0002453", + "pred" : "http://purl.obolibrary.org/obo/GALLONT_0000059", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025496" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000051", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000053", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025092" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000035", @@ -1247,9 +1400,16 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/PO_0006504" }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002453", + "propertyId" : "http://purl.obolibrary.org/obo/GALLONT_0000059", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + } ] } ] } ] } \ No newline at end of file diff --git a/gallont-base.obo b/gallont-base.obo index 680f64a..51e2c7b 100644 --- a/gallont-base.obo +++ b/gallont-base.obo @@ -1,11 +1,11 @@ format-version: 1.2 -data-version: gallont/releases/2024-04-08/gallont-base.owl +data-version: gallont/releases/2024-04-19/gallont-base.owl ontology: gallont/gallont-base 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/description "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "Plant Gall Ontology" xsd:string -property_value: owl:versionInfo "2024-04-08" xsd:string +property_value: owl:versionInfo "2024-04-19" xsd:string [Term] id: GALLONT:0000001 @@ -459,7 +459,7 @@ property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTim [Term] id: GALLONT:0000047 name: Acraspis gemula -is_a: NCBITaxon:131567 +is_a: NCBITaxon:1934078 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTime @@ -467,17 +467,57 @@ property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTim id: GALLONT:0000048 name: erineum def: "A plant gall that is induced by mites (Acariformes) on leaves and which consists of an area of leaf epidermis that has increased hairiness." [] -is_a: GALLONT:0000025 ! plant gall -is_a: OBI:0100026 +is_a: GALLONT:0000050 ! zoocecidium is_a: UBERON:0001062 intersection_of: GALLONT:0000025 ! plant gall intersection_of: BFO:0000051 PO:0006504 -intersection_of: RO:0002453 NCBITaxon:6946 +intersection_of: GALLONT:0000059 NCBITaxon:6946 ! induced by relationship: BFO:0000051 PO:0006504 -relationship: RO:0002453 NCBITaxon:6946 +relationship: GALLONT:0000059 NCBITaxon:6946 ! induced by property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T21:56:59Z" xsd:string +[Term] +id: GALLONT:0000049 +name: plant gall aggregate +name: plant gall cluster +def: "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." [] +is_a: PO:0025496 +relationship: BFO:0000051 GALLONT:0000025 ! plant gall +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-11T14:32:57Z" xsd:dateTime + +[Term] +id: GALLONT:0000050 +name: zoocecidium +def: "A plant gall that is induced by an animal" [] +is_a: GALLONT:0000025 ! plant gall +is_a: OBI:0100026 +intersection_of: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000059 NCBITaxon:33208 ! induced by +relationship: GALLONT:0000059 NCBITaxon:33208 ! induced by +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-15T13:33:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/source 978-94-017-6230-4:9 + +[Term] +id: GALLONT:0000051 +name: plant gall abscission zone +def: "An abscission zone (PO:0000146) that is part of a plant gall." [] +is_a: PO:0000146 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-18T13:34:27Z" xsd:dateTime +property_value: seeAlso https://www.inaturalist.org/observations/129032167 + +[Term] +id: GALLONT:0000053 +name: plant gall dehiscence zone +def: "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." [] +is_a: PO:0025092 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-18T14:16:58Z" xsd:dateTime +property_value: seeAlso https://www.inaturalist.org/observations/179039203 + [Typedef] id: GALLONT:0000000 name: has associate @@ -485,3 +525,16 @@ comment: Relationship that specifies which organism is associated with a class. property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-24T01:49:45Z" xsd:string +[Typedef] +id: GALLONT:0000059 +name: induced by +is_a: RO:0002440 + +[Typedef] +id: GALLONT:1000062 +name: has seasonal maturity + +[Typedef] +id: GALLONT:1000150 +name: has seasonal emergence + diff --git a/gallont-base.owl b/gallont-base.owl index cea4e07..3d0f719 100644 --- a/gallont-base.owl +++ b/gallont-base.owl @@ -11,12 +11,12 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:dcterms="http://purl.org/dc/terms/"> - + - None + Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. Plant Gall Ontology - 2024-04-08 + 2024-04-19 @@ -126,15 +126,82 @@ + + + + + induced by + + + + + + + + has seasonal maturity + + + + + + + + has seasonal emergence + + + + - + + + + + + + + + + + + + + + + 2024-03-27T01:25:52Z + hasDiameterInMm + + + + + + + + + 2024-04-11T14:02:15Z + For use with integral galls + hasLengthInMm + + + + + - + + + 2024-03-27T17:30:29Z + hasHeightInMm + @@ -901,7 +968,7 @@ - + 2024-03-25T19:40:19Z Acraspis gemula @@ -921,14 +988,13 @@ - + - - + @@ -938,7 +1004,7 @@ - + @@ -950,15 +1016,85 @@ - + - + + + + + + + + + A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation. + + 2024-04-11T14:32:57Z + plant gall aggregate + plant gall cluster + + + + + + + + + + + + + + + + + + + + + + + + + + + A plant gall that is induced by an animal + + 2024-04-15T13:33:50Z + + zoocecidium + + + + + + + + + An abscission zone (PO:0000146) that is part of a plant gall. + + + 2024-04-18T13:34:27Z + plant gall abscission zone + - + - + + + A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall. + + + 2024-04-18T14:16:58Z + plant gall dehiscence zone + + + + + + + @@ -968,12 +1104,24 @@ + + + + + + + + + + + + @@ -1118,6 +1266,12 @@ + + + + + + @@ -1139,6 +1293,12 @@ + + + + + + diff --git a/gallont-full.json b/gallont-full.json index 4f5c71e..d5a5b09 100644 --- a/gallont-full.json +++ b/gallont-full.json @@ -4,7 +4,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "None" + "val" : "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" @@ -13,9 +13,9 @@ "val" : "Plant Gall Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-08" + "val" : "2024-04-19" } ], - "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-04-08/gallont-full.json" + "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-04-19/gallont-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -1501,6 +1501,131 @@ "val" : "2023-08-01T21:56:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "lbl" : "plant gall cluster", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-11T14:32:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "lbl" : "zoocecidium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A plant gall that is induced by an animal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-15T13:33:50Z" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://doi.org/10.1007/978-94-017-6230-4_9" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000051", + "lbl" : "plant gall abscission zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abscission zone (PO:0000146) that is part of a plant gall." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/129032167" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-18T13:34:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000052", + "lbl" : "hasDiameterInMm", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-27T01:25:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000053", + "lbl" : "plant gall dehiscence zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/179039203" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-18T14:16:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "lbl" : "induced by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000041", + "lbl" : "hasLengthInMm", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "For use with integral galls" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-11T14:02:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000060", + "lbl" : "hasHeightInMm", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-27T17:30:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000062", + "lbl" : "has seasonal maturity", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000150", + "lbl" : "has seasonal emergence", + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/GO_0003674", "lbl" : "molecular_function", @@ -5861,9 +5986,6 @@ "pred" : "hasNarrowSynonym", "val" : "prothallus (narrow)", "xrefs" : [ "FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "seedling (narrow)" }, { "pred" : "hasNarrowSynonym", "val" : "shrub (narrow)" @@ -6706,6 +6828,42 @@ "val" : "plant_anatomy" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0005421", + "lbl" : "parenchyma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts.", + "xrefs" : [ "POC:curators" ] + }, + "comments" : [ "Parenchyma contains relatively unspecialized cells." ], + "subsets" : [ "http://purl.obolibrary.org/obo/po#TraitNet" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/po#Spanish", + "pred" : "hasExactSynonym", + "val" : "parénquima (Spanish, exact)", + "xrefs" : [ "POC:Maria_Alejandra_Gandolfo" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of parenchyma tissue (exact)" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of parenchymatous tissue (exact)" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Japanese", + "pred" : "hasExactSynonym", + "val" : "柔組織 (Japanese, exact)", + "xrefs" : [ "NIG:Yukiko_Yamazaki" ] + } ], + "xrefs" : [ { + "val" : "PO_GIT:107" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0005597", "lbl" : "cambium", @@ -9171,6 +9329,46 @@ "val" : "https://www.inaturalist.org/observations/60861819" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0025059", + "lbl" : "portion of ground tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).", + "xrefs" : [ "ISBN:0471244554", "ISBN:0716710072" ] + }, + "comments" : [ "Develops from the ground meristem (PO:0025594)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/po#TraitNet" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "fundamental tissue (exact)", + "xrefs" : [ "ISBN:0471244554" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Spanish", + "pred" : "hasExactSynonym", + "val" : "porción del tejido fundamental (Spanish, exact)", + "xrefs" : [ "POC:Maria_Alejandra_Gandolfo" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Japanese", + "pred" : "hasExactSynonym", + "val" : "基本組織の一部 (Japanese, exact)", + "xrefs" : [ "NIG:Yukiko_Yamazaki" ] + } ], + "xrefs" : [ { + "val" : "PO_GIT:106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "Laurel_Cooper" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-12-17T03:06:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0025060", "lbl" : "lamina", @@ -9365,6 +9563,40 @@ "val" : "plant_anatomy" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0025092", + "lbl" : "dehiscence zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.", + "xrefs" : [ "POC:curators" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/po#Spanish", + "pred" : "hasExactSynonym", + "val" : "zona de dehiscencia (Spanish, exact)", + "xrefs" : [ "POC:Maria_Alejandra_Gandolfo" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Japanese", + "pred" : "hasExactSynonym", + "val" : "裂開帯 (Japanese, exact)", + "xrefs" : [ "NIG:Yukiko_Yamazaki" ] + } ], + "xrefs" : [ { + "val" : "GO:0009900" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "rwalls" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-10-27T11:07:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0025117", "lbl" : "plant anatomical space", @@ -10446,6 +10678,29 @@ "val" : "plant_structure_development_stage" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0025594", + "lbl" : "ground meristem", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).", + "xrefs" : [ "POC:Laurel_Cooper", "POC:curators" ] + }, + "xrefs" : [ { + "val" : "PO_GIT:584" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "Laurel_Cooper" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-18T11:14:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0025606", "lbl" : "native plant cell", @@ -12413,6 +12668,23 @@ "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", @@ -12730,15 +13002,6 @@ "val" : "process_has_causal_agent" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -13063,15 +13326,6 @@ "val" : "2021-11-08T12:00:00Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0017003", - "lbl" : "positively correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between entities in which one increases or decreases as the other does the same." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0019000", "lbl" : "regulates characteristic", @@ -13148,6 +13402,10 @@ "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] } } + }, { + "id" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146", + "lbl" : "abscission zone", + "type" : "CLASS" }, { "id" : "http://purl.org/dc/terms/description", "lbl" : "description", @@ -13514,15 +13772,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000047", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { - "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", "pred" : "is_a", @@ -13533,8 +13787,36 @@ "obj" : "http://purl.obolibrary.org/obo/PO_0006504" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", - "pred" : "http://purl.obolibrary.org/obo/RO_0002453", + "pred" : "http://purl.obolibrary.org/obo/GALLONT_0000059", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025496" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000051", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000053", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025092" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0003674", "pred" : "is_a", @@ -13658,7 +13940,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6946", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6656" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6960", "pred" : "is_a", @@ -14577,6 +14859,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0000282", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0009011" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0000282", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0000282", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14613,10 +14899,18 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0005029", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025127" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0005029", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0005029", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/PO_0025433" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0005421", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025059" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0005597", "pred" : "is_a", @@ -14629,6 +14923,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0005679", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0009007" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0005679", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0005679", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -14637,6 +14935,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0006001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0009008" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0006001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0006001", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14737,6 +15039,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025496" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009001", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -14749,6 +15055,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025004" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009005", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14825,6 +15135,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009046", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025082" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009046", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009046", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -14857,6 +15171,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025023" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009062", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -15009,6 +15327,18 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025034", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0006001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009007" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025059", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/PO_0025594" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025060", "pred" : "is_a", @@ -15029,6 +15359,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025082", "pred" : "http://purl.obolibrary.org/obo/RO_0000056", "obj" : "http://purl.obolibrary.org/obo/PO_0025530" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025117", "pred" : "is_a", @@ -15041,6 +15375,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025128", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025127" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025128", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025128", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -15243,6 +15581,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025530", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025527" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025594", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009013" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025606", "pred" : "is_a", @@ -15267,6 +15609,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", "pred" : "type", @@ -15307,6 +15653,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000052", "pred" : "subPropertyOf", @@ -15419,6 +15769,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002180", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -15703,6 +16057,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002453", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002454", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002481", "pred" : "subPropertyOf", @@ -15847,10 +16205,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015007", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015006" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", @@ -16004,9 +16358,16 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/PO_0006504" }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002453", + "propertyId" : "http://purl.obolibrary.org/obo/GALLONT_0000059", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000470", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000070" ], @@ -16399,6 +16760,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/GALLONT_0000000", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GALLONT_1000062", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_03000096" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GALLONT_1000150", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_03000096" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/gallont-full.obo b/gallont-full.obo index 5b737f7..e2e55eb 100644 --- a/gallont-full.obo +++ b/gallont-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: gallont/releases/2024-04-08/gallont-full.owl +data-version: gallont/releases/2024-04-19/gallont-full.owl subsetdef: abnormal_slim "" subsetdef: absent_slim "" subsetdef: Angiosperm "" @@ -55,10 +55,10 @@ synonymtypedef: OMO:0003004 "" synonymtypedef: Spanish "" synonymtypedef: synonym "" ontology: gallont/gallont-full -property_value: http://purl.org/dc/terms/description "None" xsd:string +property_value: http://purl.org/dc/terms/description "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "Plant Gall Ontology" xsd:string -property_value: owl:versionInfo "2024-04-08" xsd:string +property_value: owl:versionInfo "2024-04-19" xsd:string [Term] id: BFO:0000001 @@ -675,7 +675,7 @@ property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTim [Term] id: GALLONT:0000047 name: Acraspis gemula -is_a: NCBITaxon:131567 ! cellular organisms +is_a: NCBITaxon:1934078 ! Acraspis property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTime @@ -683,17 +683,57 @@ property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTim id: GALLONT:0000048 name: erineum def: "A plant gall that is induced by mites (Acariformes) on leaves and which consists of an area of leaf epidermis that has increased hairiness." [] -is_a: GALLONT:0000025 ! plant gall -is_a: OBI:0100026 ! organism +is_a: GALLONT:0000050 ! zoocecidium is_a: UBERON:0001062 ! anatomical entity intersection_of: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000059 NCBITaxon:6946 ! induced by Acariformes intersection_of: has_part PO:0006504 ! leaf trichome -intersection_of: RO:0002453 NCBITaxon:6946 ! host of Acariformes +relationship: GALLONT:0000059 NCBITaxon:6946 ! induced by Acariformes relationship: has_part PO:0006504 ! leaf trichome -relationship: RO:0002453 NCBITaxon:6946 ! host of Acariformes property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T21:56:59Z" xsd:string +[Term] +id: GALLONT:0000049 +name: plant gall aggregate +name: plant gall cluster +def: "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." [] +is_a: PO:0025496 ! multi-tissue plant structure +relationship: has_part GALLONT:0000025 ! plant gall +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-11T14:32:57Z" xsd:dateTime + +[Term] +id: GALLONT:0000050 +name: zoocecidium +def: "A plant gall that is induced by an animal" [] +is_a: GALLONT:0000025 ! plant gall +is_a: OBI:0100026 ! organism +intersection_of: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000059 NCBITaxon:33208 ! induced by Metazoa +relationship: GALLONT:0000059 NCBITaxon:33208 ! induced by Metazoa +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-15T13:33:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/source 978-94-017-6230-4:9 + +[Term] +id: GALLONT:0000051 +name: plant gall abscission zone +def: "An abscission zone (PO:0000146) that is part of a plant gall." [] +is_a: PO:0000146 ! abscission zone +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-18T13:34:27Z" xsd:dateTime +property_value: seeAlso https://www.inaturalist.org/observations/129032167 + +[Term] +id: GALLONT:0000053 +name: plant gall dehiscence zone +def: "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." [] +is_a: PO:0025092 ! dehiscence zone +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-18T14:16:58Z" xsd:dateTime +property_value: seeAlso https://www.inaturalist.org/observations/179039203 + [Term] id: GO:0003674 name: gene product or complex activity @@ -1016,7 +1056,7 @@ property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6946 name: Acariformes -is_a: NCBITaxon:2759 ! Eukaryota +is_a: NCBITaxon:6656 ! Arthropoda [Term] id: NCBITaxon:6960 @@ -2899,7 +2939,6 @@ synonym: "prothalli (narrow, plural)" NARROW OMO:0003004 [FNA:4b610104-1bb0-4c6b synonym: "prothallium (narrow)" NARROW [] synonym: "prothallus (narrow)" NARROW [FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8] synonym: "ramet (broad)" BROAD [] -synonym: "seedling (narrow)" NARROW [] synonym: "shrub (narrow)" NARROW [] synonym: "sporophyte (narrow)" NARROW [] synonym: "suffrutex (narrow)" NARROW [FNA:99508f62-7116-4e2b-90c0-19ff55ebd967] @@ -3058,6 +3097,11 @@ intersection_of: PO:0006035 ! shoot system epidermis intersection_of: part_of PO:0025029 ! shoot axis relationship: part_of PO:0025029 ! shoot axis +[Term] +id: PO:0000146 +name: abscission zone +is_a: PO:0009007 ! portion of plant tissue + [Term] id: PO:0000207 name: nectary epidermis @@ -3154,6 +3198,7 @@ xref: FNA:ead20a1b-057b-4008-9466-bdb8e283aa82 xref: FNA:f18da584-2b0b-4b03-a614-40140a1cb89e xref: PO_GIT:207 is_a: PO:0009011 ! plant structure +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000349 ! plant epidermal initial cell relationship: part_of PO:0005679 ! plant epidermis @@ -3234,8 +3279,23 @@ synonym: "root primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "根原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:467 is_a: PO:0025127 ! primordium +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025433 ! root anlagen +[Term] +id: PO:0005421 +name: parenchyma +namespace: plant_anatomy +def: "A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts." [POC:curators] +comment: Parenchyma contains relatively unspecialized cells. +subset: TraitNet +synonym: "parénquima (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] +synonym: "portion of parenchyma tissue (exact)" EXACT [] +synonym: "portion of parenchymatous tissue (exact)" EXACT [] +synonym: "柔組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: PO_GIT:107 +is_a: PO:0025059 ! portion of ground tissue + [Term] id: PO:0005597 name: cambium @@ -3279,6 +3339,7 @@ synonym: "portion of epidermal tissue (exact)" EXACT [] synonym: "表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:109 is_a: PO:0009007 ! portion of plant tissue +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0006210 ! protoderm [Term] @@ -3291,6 +3352,7 @@ subset: TraitNet synonym: "filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム、葉(的）器官 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009008 ! plant organ +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025128 ! phyllome primordium relationship: part_of PO:0009006 ! shoot system @@ -3521,6 +3583,7 @@ xref: FNA:67fa41ae-b735-4d89-b5db-7631b873ef7a xref: FNA:c13b1312-1cc5-4ace-98e2-fde12aec09da xref: PO_GIT:76 is_a: PO:0025496 ! multi-tissue plant structure +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0009062 ! gynoecium property_value: seeAlso https://www.inaturalist.org/observations/138563159 @@ -3569,6 +3632,7 @@ synonym: "根 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f xref: PO_GIT:578 is_a: PO:0025004 ! plant axis +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0005029 ! root primordium relationship: part_of PO:0025025 ! root system property_value: seeAlso https://www.inaturalist.org/observations/139148692 @@ -3799,6 +3863,7 @@ synonym: "花 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:160 xref: PO_GIT:259 is_a: PO:0025082 ! reproductive shoot system +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000229 ! flower meristem [Term] @@ -3914,6 +3979,7 @@ xref: PO_GIT:470 xref: PO_GIT:71 xref: PO_GIT:98 is_a: PO:0025023 ! collective phyllome structure +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000019 ! gynoecium primordium relationship: part_of PO:0009046 ! flower @@ -4268,6 +4334,23 @@ property_value: seeAlso https://www.inaturalist.org/observations/60861819 created_by: rwalls creation_date: 2010-07-12T01:31:44Z +[Term] +id: PO:0025059 +name: portion of ground tissue +namespace: plant_anatomy +def: "Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015)." [ISBN:0471244554, ISBN:0716710072] +comment: Develops from the ground meristem (PO:0025594). +subset: TraitNet +synonym: "fundamental tissue (exact)" EXACT [ISBN:0471244554] +synonym: "porción del tejido fundamental (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] +synonym: "基本組織の一部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: PO_GIT:106 +is_a: PO:0009007 ! portion of plant tissue +is_a: UBERON:0001062 ! anatomical entity +relationship: develops_from PO:0025594 ! ground meristem +created_by: Laurel_Cooper +creation_date: 2009-12-17T03:06:13Z + [Term] id: PO:0025060 name: lamina @@ -4341,6 +4424,18 @@ relationship: participates_in PO:0025530 ! reproductive shoot system development created_by: rwalls creation_date: 2010-09-17T09:49:10Z +[Term] +id: PO:0025092 +name: dehiscence zone +namespace: plant_anatomy +def: "A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure." [POC:curators] +synonym: "zona de dehiscencia (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] +synonym: "裂開帯 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: GO:0009900 +is_a: PO:0009007 ! portion of plant tissue +created_by: rwalls +creation_date: 2010-10-27T11:07:17Z + [Term] id: PO:0025117 name: plant anatomical space @@ -4390,6 +4485,7 @@ synonym: "primordio del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejan synonym: "フィロム原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:466 is_a: PO:0025127 ! primordium +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025430 ! phyllome anlagen relationship: part_of PO:0000037 ! shoot axis apex created_by: rwalls @@ -4776,6 +4872,16 @@ is_a: PO:0025527 ! shoot system development stage created_by: Laurel_Cooper creation_date: 2012-12-13T19:01:14Z +[Term] +id: PO:0025594 +name: ground meristem +namespace: plant_anatomy +def: "A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059)." [POC:curators, POC:Laurel_Cooper] +xref: PO_GIT:584 +is_a: PO:0009013 ! portion of meristem tissue +created_by: Laurel_Cooper +creation_date: 2013-11-18T11:14:03Z + [Term] id: PO:0025606 name: native plant cell @@ -4849,6 +4955,21 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-211 property_value: http://purl.org/dc/terms/date "2024-01-24T01:49:45Z" xsd:string range: OBI:0100026 ! organism +[Typedef] +id: GALLONT:0000059 +name: induced by +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: GALLONT:1000062 +name: has seasonal maturity +range: ENVO:03000096 ! season + +[Typedef] +id: GALLONT:1000150 +name: has seasonal emergence +range: ENVO:03000096 ! season + [Typedef] id: RO:0000052 name: characteristic of @@ -5423,6 +5544,15 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with +[Typedef] +id: RO:0002454 +name: has host +def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + [Typedef] id: RO:0002464 name: helper property (not for use in curation) @@ -5563,11 +5693,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating -[Typedef] -id: RO:0002610 -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] - [Typedef] id: RO:0004031 name: enables subfunction @@ -5710,14 +5835,6 @@ property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-rel holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0017003 -name: positively correlated with -def: "A relation between entities in which one increases or decreases as the other does the same." [] -is_reflexive: true -is_symmetric: true -is_a: RO:0002610 ! correlated with - [Typedef] id: bearer_of name: bearer of @@ -5873,6 +5990,7 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: RO:0002254 ! has developmental contribution from inverse_of: RO:0002203 ! develops into [Typedef] diff --git a/gallont-full.owl b/gallont-full.owl index 0d8d698..955e0eb 100644 --- a/gallont-full.owl +++ b/gallont-full.owl @@ -21,11 +21,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - None + + Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. Plant Gall Ontology - 2024-04-08 + 2024-04-19 @@ -1129,6 +1129,33 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + induced by + + + + + + + + + has seasonal maturity + + + + + + + + + has seasonal emergence + + + + @@ -1665,6 +1692,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -2760,6 +2788,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + + + has host + http://eol.org/schema/terms/hasHost + + + + @@ -3023,15 +3064,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - correlated with - - - - @@ -3320,18 +3352,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - positively correlated with - - - - @@ -3395,6 +3415,51 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + 2024-03-27T01:25:52Z + hasDiameterInMm + + + + + + + + + + 2024-04-11T14:02:15Z + For use with integral galls + hasLengthInMm + + + + + + + + + + 2024-03-27T17:30:29Z + hasHeightInMm + + + + - + 2024-03-25T19:40:19Z Acraspis gemula @@ -4569,14 +4634,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + @@ -4586,7 +4650,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4598,6 +4662,82 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation. + + 2024-04-11T14:32:57Z + plant gall aggregate + plant gall cluster + + + + + + + + + + + + + + + + + + + + + + + + + + + A plant gall that is induced by an animal + + 2024-04-15T13:33:50Z + + zoocecidium + + + + + + + + + An abscission zone (PO:0000146) that is part of a plant gall. + + + 2024-04-18T13:34:27Z + plant gall abscission zone + + + + + + + + + A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall. + + + 2024-04-18T14:16:58Z + plant gall dehiscence zone + + + + @@ -5333,7 +5473,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Acariformes @@ -9270,7 +9410,6 @@ This issue is outside the scope of OBI. prothalli (narrow, plural) prothallium (narrow) prothallus (narrow) - seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) @@ -9992,6 +10131,7 @@ This issue is outside the scope of OBI. + @@ -10399,6 +10539,7 @@ This issue is outside the scope of OBI. + @@ -10446,6 +10587,45 @@ This issue is outside the scope of OBI. + + + + + A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts. + PO_GIT:107 + par&#233nquima (Spanish, exact) + portion of parenchyma tissue (exact) + portion of parenchymatous tissue (exact) + 柔組織 (Japanese, exact) + plant_anatomy + PO:0005421 + + Parenchyma contains relatively unspecialized cells. + parenchyma + + + + + A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts. + POC:curators + + + + + par&#233nquima (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 柔組織 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + @@ -10529,6 +10709,7 @@ This issue is outside the scope of OBI. + @@ -10592,6 +10773,7 @@ This issue is outside the scope of OBI. + @@ -11210,6 +11392,7 @@ This issue is outside the scope of OBI. + @@ -11357,6 +11540,7 @@ This issue is outside the scope of OBI. + @@ -12059,6 +12243,7 @@ This issue is outside the scope of OBI. + @@ -12315,6 +12500,7 @@ This issue is outside the scope of OBI. + @@ -13464,6 +13650,60 @@ This issue is outside the scope of OBI. + + + + + + + + + + + + Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). + Laurel_Cooper + 2009-12-17T03:06:13Z + PO_GIT:106 + fundamental tissue (exact) + porci&#243n del tejido fundamental (Spanish, exact) + 基本組織の一部 (Japanese, exact) + plant_anatomy + PO:0025059 + + Develops from the ground meristem (PO:0025594). + portion of ground tissue + + + + + Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). + ISBN:0471244554 + ISBN:0716710072 + + + + + fundamental tissue (exact) + ISBN:0471244554 + + + + + porci&#243n del tejido fundamental (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 基本組織の一部 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + @@ -13673,6 +13913,43 @@ This issue is outside the scope of OBI. + + + + + A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure. + rwalls + 2010-10-27T11:07:17Z + GO:0009900 + zona de dehiscencia (Spanish, exact) + 裂開帯 (Japanese, exact) + plant_anatomy + PO:0025092 + dehiscence zone + + + + + A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure. + POC:curators + + + + + zona de dehiscencia (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 裂開帯 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + @@ -13798,6 +14075,7 @@ This issue is outside the scope of OBI. + @@ -13920,7 +14198,7 @@ This issue is outside the scope of OBI. - + An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z @@ -13932,14 +14210,14 @@ This issue is outside the scope of OBI. Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity - + - + cjm @@ -14352,6 +14630,13 @@ This issue is outside the scope of OBI. PO:0025224 axil + + + + 腋、軸 (Japanese, exact) + NIG:Yukiko_Yamazaki + + @@ -14365,13 +14650,6 @@ This issue is outside the scope of OBI. POC:Maria_Alejandra_Gandolfo - - - - 腋、軸 (Japanese, exact) - NIG:Yukiko_Yamazaki - - @@ -15066,6 +15344,28 @@ This issue is outside the scope of OBI. + + + + + A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059). + Laurel_Cooper + 2013-11-18T11:14:03Z + PO_GIT:584 + plant_anatomy + PO:0025594 + ground meristem + + + + + A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059). + POC:Laurel_Cooper + POC:curators + + + + @@ -15215,6 +15515,15 @@ This issue is outside the scope of OBI. + + + + + abscission zone + + + + - - - - - - @@ -15452,15 +15755,6 @@ This issue is outside the scope of OBI. - - - - - - - - - @@ -15470,18 +15764,6 @@ This issue is outside the scope of OBI. - - - - - - - - - - - - @@ -15494,18 +15776,6 @@ This issue is outside the scope of OBI. - - - - - - - - - - - - @@ -15518,19 +15788,7 @@ This issue is outside the scope of OBI. - - - - - - - - - - - - - + @@ -15548,61 +15806,6 @@ This issue is outside the scope of OBI. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -15903,65 +16106,6 @@ This issue is outside the scope of OBI. 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 @@ -16019,65 +16163,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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' @@ -16137,75 +16222,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -16286,8 +16302,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16297,8 +16313,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16308,8 +16324,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16326,8 +16342,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16335,8 +16351,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 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 @@ -16366,7 +16381,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16384,7 +16399,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16394,7 +16409,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg reg edge from input to regulatory subfunction + inferring direct positive reg edge from input to regulatory subfunction @@ -16403,8 +16418,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16414,8 +16429,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16424,9 +16439,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16442,9 +16457,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16452,406 +16467,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input + effector input is compound function input @@ -17075,118 +16691,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -17343,94 +16847,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/gallont.json b/gallont.json index e3edc61..840c519 100644 --- a/gallont.json +++ b/gallont.json @@ -4,7 +4,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "None" + "val" : "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" @@ -13,9 +13,9 @@ "val" : "Plant Gall Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-08" + "val" : "2024-04-19" } ], - "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-04-08/gallont.json" + "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-04-19/gallont.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -1501,6 +1501,131 @@ "val" : "2023-08-01T21:56:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "lbl" : "plant gall cluster", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-11T14:32:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "lbl" : "zoocecidium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A plant gall that is induced by an animal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-15T13:33:50Z" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://doi.org/10.1007/978-94-017-6230-4_9" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000051", + "lbl" : "plant gall abscission zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abscission zone (PO:0000146) that is part of a plant gall." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/129032167" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-18T13:34:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000052", + "lbl" : "hasDiameterInMm", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-27T01:25:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000053", + "lbl" : "plant gall dehiscence zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/179039203" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-18T14:16:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "lbl" : "induced by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000041", + "lbl" : "hasLengthInMm", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "For use with integral galls" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-04-11T14:02:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000060", + "lbl" : "hasHeightInMm", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-27T17:30:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000062", + "lbl" : "has seasonal maturity", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_1000150", + "lbl" : "has seasonal emergence", + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/GO_0003674", "lbl" : "molecular_function", @@ -5861,9 +5986,6 @@ "pred" : "hasNarrowSynonym", "val" : "prothallus (narrow)", "xrefs" : [ "FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "seedling (narrow)" }, { "pred" : "hasNarrowSynonym", "val" : "shrub (narrow)" @@ -6706,6 +6828,42 @@ "val" : "plant_anatomy" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0005421", + "lbl" : "parenchyma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts.", + "xrefs" : [ "POC:curators" ] + }, + "comments" : [ "Parenchyma contains relatively unspecialized cells." ], + "subsets" : [ "http://purl.obolibrary.org/obo/po#TraitNet" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/po#Spanish", + "pred" : "hasExactSynonym", + "val" : "parénquima (Spanish, exact)", + "xrefs" : [ "POC:Maria_Alejandra_Gandolfo" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of parenchyma tissue (exact)" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of parenchymatous tissue (exact)" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Japanese", + "pred" : "hasExactSynonym", + "val" : "柔組織 (Japanese, exact)", + "xrefs" : [ "NIG:Yukiko_Yamazaki" ] + } ], + "xrefs" : [ { + "val" : "PO_GIT:107" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0005597", "lbl" : "cambium", @@ -9171,6 +9329,46 @@ "val" : "https://www.inaturalist.org/observations/60861819" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0025059", + "lbl" : "portion of ground tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).", + "xrefs" : [ "ISBN:0471244554", "ISBN:0716710072" ] + }, + "comments" : [ "Develops from the ground meristem (PO:0025594)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/po#TraitNet" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "fundamental tissue (exact)", + "xrefs" : [ "ISBN:0471244554" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Spanish", + "pred" : "hasExactSynonym", + "val" : "porción del tejido fundamental (Spanish, exact)", + "xrefs" : [ "POC:Maria_Alejandra_Gandolfo" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Japanese", + "pred" : "hasExactSynonym", + "val" : "基本組織の一部 (Japanese, exact)", + "xrefs" : [ "NIG:Yukiko_Yamazaki" ] + } ], + "xrefs" : [ { + "val" : "PO_GIT:106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "Laurel_Cooper" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-12-17T03:06:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0025060", "lbl" : "lamina", @@ -9365,6 +9563,40 @@ "val" : "plant_anatomy" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0025092", + "lbl" : "dehiscence zone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.", + "xrefs" : [ "POC:curators" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/po#Spanish", + "pred" : "hasExactSynonym", + "val" : "zona de dehiscencia (Spanish, exact)", + "xrefs" : [ "POC:Maria_Alejandra_Gandolfo" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/po#Japanese", + "pred" : "hasExactSynonym", + "val" : "裂開帯 (Japanese, exact)", + "xrefs" : [ "NIG:Yukiko_Yamazaki" ] + } ], + "xrefs" : [ { + "val" : "GO:0009900" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "rwalls" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-10-27T11:07:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0025117", "lbl" : "plant anatomical space", @@ -10446,6 +10678,29 @@ "val" : "plant_structure_development_stage" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PO_0025594", + "lbl" : "ground meristem", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).", + "xrefs" : [ "POC:Laurel_Cooper", "POC:curators" ] + }, + "xrefs" : [ { + "val" : "PO_GIT:584" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "Laurel_Cooper" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-18T11:14:03Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "plant_anatomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PO_0025606", "lbl" : "native plant cell", @@ -12413,6 +12668,23 @@ "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", @@ -12730,15 +13002,6 @@ "val" : "process_has_causal_agent" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -13063,15 +13326,6 @@ "val" : "2021-11-08T12:00:00Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0017003", - "lbl" : "positively correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between entities in which one increases or decreases as the other does the same." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0019000", "lbl" : "regulates characteristic", @@ -13148,6 +13402,10 @@ "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] } } + }, { + "id" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146", + "lbl" : "abscission zone", + "type" : "CLASS" }, { "id" : "http://purl.org/dc/terms/description", "lbl" : "description", @@ -13514,15 +13772,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000047", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { - "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", "pred" : "is_a", @@ -13533,8 +13787,36 @@ "obj" : "http://purl.obolibrary.org/obo/PO_0006504" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000048", - "pred" : "http://purl.obolibrary.org/obo/RO_0002453", + "pred" : "http://purl.obolibrary.org/obo/GALLONT_0000059", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025496" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000049", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "pred" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000051", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000053", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025092" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0003674", "pred" : "is_a", @@ -13658,7 +13940,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6946", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6656" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6960", "pred" : "is_a", @@ -14577,6 +14859,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0000282", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0009011" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0000282", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0000282", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14613,10 +14899,18 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0005029", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025127" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0005029", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0005029", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/PO_0025433" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0005421", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025059" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0005597", "pred" : "is_a", @@ -14629,6 +14923,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0005679", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0009007" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0005679", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0005679", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -14637,6 +14935,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0006001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0009008" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0006001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0006001", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14737,6 +15039,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025496" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009001", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -14749,6 +15055,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025004" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009005", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14825,6 +15135,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009046", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025082" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009046", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009046", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -14857,6 +15171,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0009062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025023" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0009062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0009062", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -15009,6 +15327,18 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025034", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0006001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009007" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025059", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/PO_0025594" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025060", "pred" : "is_a", @@ -15029,6 +15359,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025082", "pred" : "http://purl.obolibrary.org/obo/RO_0000056", "obj" : "http://purl.obolibrary.org/obo/PO_0025530" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025117", "pred" : "is_a", @@ -15041,6 +15375,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025128", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025127" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025128", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025128", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -15243,6 +15581,10 @@ "sub" : "http://purl.obolibrary.org/obo/PO_0025530", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025527" + }, { + "sub" : "http://purl.obolibrary.org/obo/PO_0025594", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009013" }, { "sub" : "http://purl.obolibrary.org/obo/PO_0025606", "pred" : "is_a", @@ -15267,6 +15609,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/PO_0000146", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", "pred" : "type", @@ -15307,6 +15653,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000052", "pred" : "subPropertyOf", @@ -15419,6 +15769,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002180", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -15703,6 +16057,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002453", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002454", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002481", "pred" : "subPropertyOf", @@ -15847,10 +16205,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015007", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015006" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", @@ -16004,9 +16358,16 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/PO_0006504" }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002453", + "propertyId" : "http://purl.obolibrary.org/obo/GALLONT_0000059", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000050", + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GALLONT_0000059", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000470", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000070" ], @@ -16399,6 +16760,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/GALLONT_0000000", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GALLONT_1000062", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_03000096" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GALLONT_1000150", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_03000096" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/gallont.obo b/gallont.obo index 113b32b..08af9aa 100644 --- a/gallont.obo +++ b/gallont.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-04-08 +data-version: releases/2024-04-19 subsetdef: abnormal_slim "" subsetdef: absent_slim "" subsetdef: Angiosperm "" @@ -55,10 +55,10 @@ synonymtypedef: OMO:0003004 "" synonymtypedef: Spanish "" synonymtypedef: synonym "" ontology: gallont -property_value: http://purl.org/dc/terms/description "None" xsd:string +property_value: http://purl.org/dc/terms/description "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "Plant Gall Ontology" xsd:string -property_value: owl:versionInfo "2024-04-08" xsd:string +property_value: owl:versionInfo "2024-04-19" xsd:string [Term] id: BFO:0000001 @@ -675,7 +675,7 @@ property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTim [Term] id: GALLONT:0000047 name: Acraspis gemula -is_a: NCBITaxon:131567 ! cellular organisms +is_a: NCBITaxon:1934078 ! Acraspis property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTime @@ -683,17 +683,57 @@ property_value: http://purl.org/dc/terms/date "2024-03-25T19:40:19Z" xsd:dateTim id: GALLONT:0000048 name: erineum def: "A plant gall that is induced by mites (Acariformes) on leaves and which consists of an area of leaf epidermis that has increased hairiness." [] -is_a: GALLONT:0000025 ! plant gall -is_a: OBI:0100026 ! organism +is_a: GALLONT:0000050 ! zoocecidium is_a: UBERON:0001062 ! anatomical entity intersection_of: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000059 NCBITaxon:6946 ! induced by Acariformes intersection_of: has_part PO:0006504 ! leaf trichome -intersection_of: RO:0002453 NCBITaxon:6946 ! host of Acariformes +relationship: GALLONT:0000059 NCBITaxon:6946 ! induced by Acariformes relationship: has_part PO:0006504 ! leaf trichome -relationship: RO:0002453 NCBITaxon:6946 ! host of Acariformes property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T21:56:59Z" xsd:string +[Term] +id: GALLONT:0000049 +name: plant gall aggregate +name: plant gall cluster +def: "A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation." [] +is_a: PO:0025496 ! multi-tissue plant structure +relationship: has_part GALLONT:0000025 ! plant gall +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-11T14:32:57Z" xsd:dateTime + +[Term] +id: GALLONT:0000050 +name: zoocecidium +def: "A plant gall that is induced by an animal" [] +is_a: GALLONT:0000025 ! plant gall +is_a: OBI:0100026 ! organism +intersection_of: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000059 NCBITaxon:33208 ! induced by Metazoa +relationship: GALLONT:0000059 NCBITaxon:33208 ! induced by Metazoa +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-15T13:33:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/source 978-94-017-6230-4:9 + +[Term] +id: GALLONT:0000051 +name: plant gall abscission zone +def: "An abscission zone (PO:0000146) that is part of a plant gall." [] +is_a: PO:0000146 ! abscission zone +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-18T13:34:27Z" xsd:dateTime +property_value: seeAlso https://www.inaturalist.org/observations/129032167 + +[Term] +id: GALLONT:0000053 +name: plant gall dehiscence zone +def: "A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall." [] +is_a: PO:0025092 ! dehiscence zone +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-04-18T14:16:58Z" xsd:dateTime +property_value: seeAlso https://www.inaturalist.org/observations/179039203 + [Term] id: GO:0003674 name: gene product or complex activity @@ -1016,7 +1056,7 @@ property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6946 name: Acariformes -is_a: NCBITaxon:2759 ! Eukaryota +is_a: NCBITaxon:6656 ! Arthropoda [Term] id: NCBITaxon:6960 @@ -2899,7 +2939,6 @@ synonym: "prothalli (narrow, plural)" NARROW OMO:0003004 [FNA:4b610104-1bb0-4c6b synonym: "prothallium (narrow)" NARROW [] synonym: "prothallus (narrow)" NARROW [FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8] synonym: "ramet (broad)" BROAD [] -synonym: "seedling (narrow)" NARROW [] synonym: "shrub (narrow)" NARROW [] synonym: "sporophyte (narrow)" NARROW [] synonym: "suffrutex (narrow)" NARROW [FNA:99508f62-7116-4e2b-90c0-19ff55ebd967] @@ -3058,6 +3097,11 @@ intersection_of: PO:0006035 ! shoot system epidermis intersection_of: part_of PO:0025029 ! shoot axis relationship: part_of PO:0025029 ! shoot axis +[Term] +id: PO:0000146 +name: abscission zone +is_a: PO:0009007 ! portion of plant tissue + [Term] id: PO:0000207 name: nectary epidermis @@ -3154,6 +3198,7 @@ xref: FNA:ead20a1b-057b-4008-9466-bdb8e283aa82 xref: FNA:f18da584-2b0b-4b03-a614-40140a1cb89e xref: PO_GIT:207 is_a: PO:0009011 ! plant structure +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000349 ! plant epidermal initial cell relationship: part_of PO:0005679 ! plant epidermis @@ -3234,8 +3279,23 @@ synonym: "root primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "根原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:467 is_a: PO:0025127 ! primordium +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025433 ! root anlagen +[Term] +id: PO:0005421 +name: parenchyma +namespace: plant_anatomy +def: "A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts." [POC:curators] +comment: Parenchyma contains relatively unspecialized cells. +subset: TraitNet +synonym: "parénquima (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] +synonym: "portion of parenchyma tissue (exact)" EXACT [] +synonym: "portion of parenchymatous tissue (exact)" EXACT [] +synonym: "柔組織 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: PO_GIT:107 +is_a: PO:0025059 ! portion of ground tissue + [Term] id: PO:0005597 name: cambium @@ -3279,6 +3339,7 @@ synonym: "portion of epidermal tissue (exact)" EXACT [] synonym: "表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:109 is_a: PO:0009007 ! portion of plant tissue +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0006210 ! protoderm [Term] @@ -3291,6 +3352,7 @@ subset: TraitNet synonym: "filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム、葉(的）器官 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009008 ! plant organ +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025128 ! phyllome primordium relationship: part_of PO:0009006 ! shoot system @@ -3521,6 +3583,7 @@ xref: FNA:67fa41ae-b735-4d89-b5db-7631b873ef7a xref: FNA:c13b1312-1cc5-4ace-98e2-fde12aec09da xref: PO_GIT:76 is_a: PO:0025496 ! multi-tissue plant structure +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0009062 ! gynoecium property_value: seeAlso https://www.inaturalist.org/observations/138563159 @@ -3569,6 +3632,7 @@ synonym: "根 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f xref: PO_GIT:578 is_a: PO:0025004 ! plant axis +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0005029 ! root primordium relationship: part_of PO:0025025 ! root system property_value: seeAlso https://www.inaturalist.org/observations/139148692 @@ -3799,6 +3863,7 @@ synonym: "花 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:160 xref: PO_GIT:259 is_a: PO:0025082 ! reproductive shoot system +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000229 ! flower meristem [Term] @@ -3914,6 +3979,7 @@ xref: PO_GIT:470 xref: PO_GIT:71 xref: PO_GIT:98 is_a: PO:0025023 ! collective phyllome structure +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0000019 ! gynoecium primordium relationship: part_of PO:0009046 ! flower @@ -4268,6 +4334,23 @@ property_value: seeAlso https://www.inaturalist.org/observations/60861819 created_by: rwalls creation_date: 2010-07-12T01:31:44Z +[Term] +id: PO:0025059 +name: portion of ground tissue +namespace: plant_anatomy +def: "Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015)." [ISBN:0471244554, ISBN:0716710072] +comment: Develops from the ground meristem (PO:0025594). +subset: TraitNet +synonym: "fundamental tissue (exact)" EXACT [ISBN:0471244554] +synonym: "porción del tejido fundamental (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] +synonym: "基本組織の一部 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: PO_GIT:106 +is_a: PO:0009007 ! portion of plant tissue +is_a: UBERON:0001062 ! anatomical entity +relationship: develops_from PO:0025594 ! ground meristem +created_by: Laurel_Cooper +creation_date: 2009-12-17T03:06:13Z + [Term] id: PO:0025060 name: lamina @@ -4341,6 +4424,18 @@ relationship: participates_in PO:0025530 ! reproductive shoot system development created_by: rwalls creation_date: 2010-09-17T09:49:10Z +[Term] +id: PO:0025092 +name: dehiscence zone +namespace: plant_anatomy +def: "A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure." [POC:curators] +synonym: "zona de dehiscencia (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] +synonym: "裂開帯 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: GO:0009900 +is_a: PO:0009007 ! portion of plant tissue +created_by: rwalls +creation_date: 2010-10-27T11:07:17Z + [Term] id: PO:0025117 name: plant anatomical space @@ -4390,6 +4485,7 @@ synonym: "primordio del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejan synonym: "フィロム原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:466 is_a: PO:0025127 ! primordium +is_a: UBERON:0001062 ! anatomical entity relationship: develops_from PO:0025430 ! phyllome anlagen relationship: part_of PO:0000037 ! shoot axis apex created_by: rwalls @@ -4776,6 +4872,16 @@ is_a: PO:0025527 ! shoot system development stage created_by: Laurel_Cooper creation_date: 2012-12-13T19:01:14Z +[Term] +id: PO:0025594 +name: ground meristem +namespace: plant_anatomy +def: "A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059)." [POC:curators, POC:Laurel_Cooper] +xref: PO_GIT:584 +is_a: PO:0009013 ! portion of meristem tissue +created_by: Laurel_Cooper +creation_date: 2013-11-18T11:14:03Z + [Term] id: PO:0025606 name: native plant cell @@ -4849,6 +4955,21 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-211 property_value: http://purl.org/dc/terms/date "2024-01-24T01:49:45Z" xsd:string range: OBI:0100026 ! organism +[Typedef] +id: GALLONT:0000059 +name: induced by +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: GALLONT:1000062 +name: has seasonal maturity +range: ENVO:03000096 ! season + +[Typedef] +id: GALLONT:1000150 +name: has seasonal emergence +range: ENVO:03000096 ! season + [Typedef] id: RO:0000052 name: characteristic of @@ -5423,6 +5544,15 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with +[Typedef] +id: RO:0002454 +name: has host +def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + [Typedef] id: RO:0002464 name: helper property (not for use in curation) @@ -5563,11 +5693,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating -[Typedef] -id: RO:0002610 -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] - [Typedef] id: RO:0004031 name: enables subfunction @@ -5710,14 +5835,6 @@ property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-rel holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0017003 -name: positively correlated with -def: "A relation between entities in which one increases or decreases as the other does the same." [] -is_reflexive: true -is_symmetric: true -is_a: RO:0002610 ! correlated with - [Typedef] id: bearer_of name: bearer of @@ -5873,6 +5990,7 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: RO:0002254 ! has developmental contribution from inverse_of: RO:0002203 ! develops into [Typedef] diff --git a/gallont.owl b/gallont.owl index 6b1a6e7..6b755c1 100644 --- a/gallont.owl +++ b/gallont.owl @@ -21,11 +21,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - None + + Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. Plant Gall Ontology - 2024-04-08 + 2024-04-19 @@ -1129,6 +1129,33 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + induced by + + + + + + + + + has seasonal maturity + + + + + + + + + has seasonal emergence + + + + @@ -1665,6 +1692,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -2760,6 +2788,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + + + has host + http://eol.org/schema/terms/hasHost + + + + @@ -3023,15 +3064,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - correlated with - - - - @@ -3320,18 +3352,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - positively correlated with - - - - @@ -3395,6 +3415,51 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + 2024-03-27T01:25:52Z + hasDiameterInMm + + + + + + + + + + 2024-04-11T14:02:15Z + For use with integral galls + hasLengthInMm + + + + + + + + + + 2024-03-27T17:30:29Z + hasHeightInMm + + + + - + 2024-03-25T19:40:19Z Acraspis gemula @@ -4569,14 +4634,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + @@ -4586,7 +4650,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4598,6 +4662,82 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation. + + 2024-04-11T14:32:57Z + plant gall aggregate + plant gall cluster + + + + + + + + + + + + + + + + + + + + + + + + + + + A plant gall that is induced by an animal + + 2024-04-15T13:33:50Z + + zoocecidium + + + + + + + + + An abscission zone (PO:0000146) that is part of a plant gall. + + + 2024-04-18T13:34:27Z + plant gall abscission zone + + + + + + + + + A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall. + + + 2024-04-18T14:16:58Z + plant gall dehiscence zone + + + + @@ -5333,7 +5473,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Acariformes @@ -9270,7 +9410,6 @@ This issue is outside the scope of OBI. prothalli (narrow, plural) prothallium (narrow) prothallus (narrow) - seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) @@ -9992,6 +10131,7 @@ This issue is outside the scope of OBI. + @@ -10399,6 +10539,7 @@ This issue is outside the scope of OBI. + @@ -10446,6 +10587,45 @@ This issue is outside the scope of OBI. + + + + + A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts. + PO_GIT:107 + par&#233nquima (Spanish, exact) + portion of parenchyma tissue (exact) + portion of parenchymatous tissue (exact) + 柔組織 (Japanese, exact) + plant_anatomy + PO:0005421 + + Parenchyma contains relatively unspecialized cells. + parenchyma + + + + + A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts. + POC:curators + + + + + par&#233nquima (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 柔組織 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + @@ -10529,6 +10709,7 @@ This issue is outside the scope of OBI. + @@ -10592,6 +10773,7 @@ This issue is outside the scope of OBI. + @@ -11210,6 +11392,7 @@ This issue is outside the scope of OBI. + @@ -11357,6 +11540,7 @@ This issue is outside the scope of OBI. + @@ -12059,6 +12243,7 @@ This issue is outside the scope of OBI. + @@ -12315,6 +12500,7 @@ This issue is outside the scope of OBI. + @@ -13464,6 +13650,60 @@ This issue is outside the scope of OBI. + + + + + + + + + + + + Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). + Laurel_Cooper + 2009-12-17T03:06:13Z + PO_GIT:106 + fundamental tissue (exact) + porci&#243n del tejido fundamental (Spanish, exact) + 基本組織の一部 (Japanese, exact) + plant_anatomy + PO:0025059 + + Develops from the ground meristem (PO:0025594). + portion of ground tissue + + + + + Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). + ISBN:0471244554 + ISBN:0716710072 + + + + + fundamental tissue (exact) + ISBN:0471244554 + + + + + porci&#243n del tejido fundamental (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 基本組織の一部 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + @@ -13673,6 +13913,43 @@ This issue is outside the scope of OBI. + + + + + A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure. + rwalls + 2010-10-27T11:07:17Z + GO:0009900 + zona de dehiscencia (Spanish, exact) + 裂開帯 (Japanese, exact) + plant_anatomy + PO:0025092 + dehiscence zone + + + + + A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure. + POC:curators + + + + + zona de dehiscencia (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 裂開帯 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + @@ -13798,6 +14075,7 @@ This issue is outside the scope of OBI. + @@ -13920,7 +14198,7 @@ This issue is outside the scope of OBI. - + An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z @@ -13932,14 +14210,14 @@ This issue is outside the scope of OBI. Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity - + - + cjm @@ -14236,6 +14514,13 @@ This issue is outside the scope of OBI. PO:0025206 phyllome vascular system + + + + フィロム維管系 (Japanese, exact) + NIG:Yukiko_Yamazaki + + @@ -14249,13 +14534,6 @@ This issue is outside the scope of OBI. POC:Maria_Alejandra_Gandolfo - - - - フィロム維管系 (Japanese, exact) - NIG:Yukiko_Yamazaki - - @@ -14434,13 +14712,6 @@ This issue is outside the scope of OBI. Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). collective plant organ structure development stage - - - - 集合的植物構造の発生過程 (Japanese, exact) - NIG:Yukiko_Yamazaki - - @@ -14454,6 +14725,13 @@ This issue is outside the scope of OBI. POC:Maria_Alejandra_Gandolfo + + + + 集合的植物構造の発生過程 (Japanese, exact) + NIG:Yukiko_Yamazaki + + @@ -15066,6 +15344,28 @@ This issue is outside the scope of OBI. + + + + + A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059). + Laurel_Cooper + 2013-11-18T11:14:03Z + PO_GIT:584 + plant_anatomy + PO:0025594 + ground meristem + + + + + A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059). + POC:Laurel_Cooper + POC:curators + + + + @@ -15215,6 +15515,15 @@ This issue is outside the scope of OBI. + + + + + abscission zone + + + + - - - - - - @@ -15452,15 +15755,6 @@ This issue is outside the scope of OBI. - - - - - - - - - @@ -15470,42 +15764,18 @@ This issue is outside the scope of OBI. - + - + - - - - - - - - - - - - - + - - - - - - - - - - - - @@ -15518,18 +15788,6 @@ This issue is outside the scope of OBI. - - - - - - - - - - - - @@ -15548,61 +15806,6 @@ This issue is outside the scope of OBI. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -15903,65 +16106,6 @@ This issue is outside the scope of OBI. 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 @@ -16019,65 +16163,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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' @@ -16146,8 +16231,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16157,7 +16242,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16167,8 +16252,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16178,8 +16263,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16198,8 +16283,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16207,6 +16292,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + 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 @@ -16214,9 +16301,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16224,9 +16311,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + @@ -16235,25 +16323,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -16266,9 +16341,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16276,8 +16351,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 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 @@ -16286,8 +16360,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16297,8 +16371,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16307,9 +16381,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16325,9 +16399,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16335,8 +16409,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 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 positive reg edge from input to regulatory subfunction @@ -16366,7 +16439,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16384,7 +16457,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16394,464 +16467,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input + effector input is compound function input @@ -17075,118 +16691,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -17343,94 +16847,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index 67df8c7..10c60c3 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-08") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 190ed95..c75fec7 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-08") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/po_import.owl b/src/ontology/imports/po_import.owl index 86c0031..9a049bf 100644 --- a/src/ontology/imports/po_import.owl +++ b/src/ontology/imports/po_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-04-08") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) @@ -53,6 +53,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -109,10 +110,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -144,6 +147,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -251,7 +255,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -265,7 +268,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -457,7 +459,7 @@ AnnotationAssertion(rdfs:label (part_of) +# Object Property: (part of) AnnotationAssertion( "a core relation that holds between a part and its whole"@en) AnnotationAssertion( "BFO:0000050") @@ -465,6 +467,7 @@ AnnotationAssertion( "part_of") AnnotationAssertion( "part_of") AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:label "part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -478,14 +481,15 @@ AnnotationAssertion( "has_part") AnnotationAssertion( "has_part") AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") AnnotationAssertion(rdfs:label "has_part") SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (preceded by) +# Object Property: (preceded_by) -AnnotationAssertion(Annotation( "POC:Laurel_Cooper") "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.") AnnotationAssertion( "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."@en) +AnnotationAssertion(Annotation( "POC:Laurel_Cooper") "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.") AnnotationAssertion( "Laurel_Cooper") AnnotationAssertion( "2013-07-09T14:29:15Z") AnnotationAssertion( "BFO:0000062") @@ -510,8 +514,8 @@ AnnotationAssertion( "plant_ontology") AnnotationAssertion( "precedes") AnnotationAssertion( "precedes") -AnnotationAssertion(rdfs:label "precedes") AnnotationAssertion(rdfs:label "precedes"@en) +AnnotationAssertion(rdfs:label "precedes") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -525,10 +529,11 @@ SubObjectPropertyOf( ) FunctionalObjectProperty() -# Object Property: (bearer of) +# Object Property: (has characteristic) AnnotationAssertion( "Inverse of characteristic_of"@en) AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "has characteristic") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -545,7 +550,7 @@ InverseObjectProperties( ) ObjectPropertyRange( ) -# Object Property: (has participant) +# Object Property: (has_participant) AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "RO:0000057") @@ -553,8 +558,10 @@ AnnotationAssertion( "has_participant") AnnotationAssertion( "has_participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") AnnotationAssertion(rdfs:label "has_participant") ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (function of) @@ -702,7 +709,7 @@ AnnotationAssertion(rdfs:label "over SubObjectPropertyOf( ) SymmetricObjectProperty() -# Object Property: (only in taxon) +# Object Property: (only_in_taxon) AnnotationAssertion( "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.") AnnotationAssertion( "RO:0002160") @@ -735,6 +742,7 @@ AnnotationAssertion( "develops_from") AnnotationAssertion(rdfs:label "develops from"@en) AnnotationAssertion(rdfs:label "develops_from") +SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -922,6 +930,7 @@ SubObjectPropertyOf( "inverse of enables") AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:label "enabled by") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1231,11 +1240,6 @@ AnnotationAssertion( "process has causal agent") SubObjectPropertyOf( ) -# Object Property: (correlated with) - -AnnotationAssertion( "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.") -AnnotationAssertion(rdfs:label "correlated with") - # Object Property: (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") @@ -1317,14 +1321,6 @@ AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - # Object Property: (regulates characteristic) AnnotationAssertion( "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.") @@ -1379,6 +1375,7 @@ DisjointClasses( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) # Class: (disposition) @@ -1389,6 +1386,7 @@ DisjointClasses( (realizable entity) AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "realizable"@en) AnnotationAssertion(rdfs:label "realizable entity"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1400,12 +1398,14 @@ AnnotationAssertion(rdfs:label "qua SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -# Class: (specifically dependent continuant) +# Class: (characteristic) AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(rdfs:label "characteristic"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (role) @@ -1428,16 +1428,23 @@ SubClassOf( "GOC:pdt") "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.") AnnotationAssertion( "molecular function") +AnnotationAssertion(rdfs:label "gene product or complex activity"@en) AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) # Class: (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "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.") +AnnotationAssertion( "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.") AnnotationAssertion( "biological process") AnnotationAssertion( "physiological process") AnnotationAssertion( "single organism process") AnnotationAssertion( "single-organism process") +AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kinase activity) @@ -1524,7 +1531,6 @@ AnnotationAssertion( "FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0") Annotation( ) "prothalli (narrow, plural)") AnnotationAssertion( "prothallium (narrow)") AnnotationAssertion(Annotation( "FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8") "prothallus (narrow)") -AnnotationAssertion( "seedling (narrow)") AnnotationAssertion( "shrub (narrow)") AnnotationAssertion( "sporophyte (narrow)") AnnotationAssertion(Annotation( "FNA:99508f62-7116-4e2b-90c0-19ff55ebd967") "suffrutex (narrow)") @@ -1874,6 +1880,21 @@ AnnotationAssertion(rdfs:label "root SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (parenchyma) + +AnnotationAssertion(Annotation( "POC:curators") "A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts.") +AnnotationAssertion( "PO_GIT:107") +AnnotationAssertion(Annotation( "POC:Maria_Alejandra_Gandolfo") Annotation( ) "parénquima (Spanish, exact)") +AnnotationAssertion( "portion of parenchyma tissue (exact)") +AnnotationAssertion( "portion of parenchymatous tissue (exact)") +AnnotationAssertion(Annotation( "NIG:Yukiko_Yamazaki") Annotation( ) "柔組織 (Japanese, exact)") +AnnotationAssertion( "plant_anatomy") +AnnotationAssertion( "PO:0005421") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Parenchyma contains relatively unspecialized cells.") +AnnotationAssertion(rdfs:label "parenchyma") +SubClassOf( ) + # Class: (cambium) AnnotationAssertion(Annotation( "ISBN:047125208") "A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.") @@ -1965,7 +1986,7 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (adaxial leaf epidermis) +# Class: (leaf adaxial epidermis) AnnotationAssertion(Annotation( "POC:Ramona_Walls") "A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf (PO:0025034).") AnnotationAssertion(Annotation( "POC:Maria_Alejandra_Gandolfo") Annotation( ) "epidermis adaxial de la hoja (Spanish, exact)") @@ -1977,7 +1998,7 @@ AnnotationAssertion(rdfs:comment "Us AnnotationAssertion(rdfs:label "leaf adaxial epidermis") SubClassOf( ) -# Class: (abaxial leaf epidermis) +# Class: (leaf abaxial epidermis) AnnotationAssertion(Annotation( "POC:Laurel_Cooper") Annotation( "POC:curators") "A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf (PO:0025034).") AnnotationAssertion(Annotation( "POC:Maria_Alejandra_Gandolfo") Annotation( ) "epidermis abaxial de la hoja (Spanish, exact)") @@ -2518,6 +2539,7 @@ AnnotationAssertion( "An inflorescence is a reproductive shoot system from which at least two flowers develop. The growth pattern of an inflorescence may be monopodial (single main shoot axis), sympodial (growth only occurs from axillary meristems), or both. An inflorescence axis (PO:0020122) can be determinate or indeterminate. An inflorescence flower pedicel (PO:0009052) is the ultimate axis in an inflorescence. The flower (PO:0009046) of many plants, for example Magnolia spp., is solitary.") AnnotationAssertion(rdfs:label "inflorescence") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -2652,7 +2674,7 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (leaf vein) +# Class: (leaf lamina vein) AnnotationAssertion(Annotation( "POC:curators") "A phyllome lamina vein (PO:0025348) that is part of a leaf lamina vascular system (PO:0000048).") AnnotationAssertion( "PO_GIT:410") @@ -2918,6 +2940,23 @@ AnnotationAssertion( "leaf") SubClassOf( ) +# Class: (portion of ground tissue) + +AnnotationAssertion(Annotation( "ISBN:0471244554") Annotation( "ISBN:0716710072") "Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).") +AnnotationAssertion( "Laurel_Cooper") +AnnotationAssertion( "2009-12-17T03:06:13Z") +AnnotationAssertion( "PO_GIT:106") +AnnotationAssertion(Annotation( "ISBN:0471244554") "fundamental tissue (exact)") +AnnotationAssertion(Annotation( "POC:Maria_Alejandra_Gandolfo") Annotation( ) "porción del tejido fundamental (Spanish, exact)") +AnnotationAssertion(Annotation( "NIG:Yukiko_Yamazaki") Annotation( ) "基本組織の一部 (Japanese, exact)") +AnnotationAssertion( "plant_anatomy") +AnnotationAssertion( "PO:0025059") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Develops from the ground meristem (PO:0025594).") +AnnotationAssertion(rdfs:label "portion of ground tissue") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (lamina) AnnotationAssertion(Annotation( "POC:curators") "A cardinal part of multi-tissue plant structure (PO:0025498) that is thin and flat.") @@ -2992,6 +3031,19 @@ AnnotationAssertion(rdfs:label "repr SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (dehiscence zone) + +AnnotationAssertion(Annotation( "POC:curators") "A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.") +AnnotationAssertion( "rwalls") +AnnotationAssertion( "2010-10-27T11:07:17Z") +AnnotationAssertion( "GO:0009900") +AnnotationAssertion(Annotation( "POC:Maria_Alejandra_Gandolfo") Annotation( ) "zona de dehiscencia (Spanish, exact)") +AnnotationAssertion(Annotation( "NIG:Yukiko_Yamazaki") Annotation( ) "裂開帯 (Japanese, exact)") +AnnotationAssertion( "plant_anatomy") +AnnotationAssertion( "PO:0025092") +AnnotationAssertion(rdfs:label "dehiscence zone") +SubClassOf( ) + # Class: (plant anatomical space) AnnotationAssertion(Annotation( "CARO:0000005") Annotation( "PO:cooperl") Annotation( "POC:curators") "An anatomical space that is part of a plant.") @@ -3450,6 +3502,17 @@ AnnotationAssertion( "reproductive shoot system development stage") SubClassOf( ) +# Class: (ground meristem) + +AnnotationAssertion(Annotation( "POC:Laurel_Cooper") Annotation( "POC:curators") "A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).") +AnnotationAssertion( "Laurel_Cooper") +AnnotationAssertion( "2013-11-18T11:14:03Z") +AnnotationAssertion( "PO_GIT:584") +AnnotationAssertion( "plant_anatomy") +AnnotationAssertion( "PO:0025594") +AnnotationAssertion(rdfs:label "ground meristem") +SubClassOf( ) + # Class: (native plant cell) AnnotationAssertion(Annotation( "POC:Laurel_Cooper") "A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).") @@ -3630,30 +3693,30 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +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'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 9127641..4e1bbfb 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-08") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) @@ -103,6 +103,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -1190,6 +1191,15 @@ AnnotationAssertion( "host of") SubObjectPropertyOf( ) +# Object Property: (has host) + +AnnotationAssertion( "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has host") +AnnotationAssertion(rdfs:seeAlso "http://eol.org/schema/terms/hasHost") +SubObjectPropertyOf( ) + # Object Property: (helper property (not for use in curation)) AnnotationAssertion( )