diff --git a/gallont-base.json b/gallont-base.json index 80b9480..e5984f1 100644 --- a/gallont-base.json +++ b/gallont-base.json @@ -16,9 +16,9 @@ "val" : "Plant Gall Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-03-14" + "val" : "2024-03-25" } ], - "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-03-14/gallont-base.json" + "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-03-25/gallont-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000000", @@ -36,22 +36,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000001", - "lbl" : "plant gall", + "lbl" : "DEPRECATED plant gall", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism." - }, + "comments" : [ "Updated the class definition to reflect that this structure is a response to biotic stress" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-2119-4663" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-06-19T19:39:13Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.inaturalist.org/observations/62135900" - } ] + "val" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000002", @@ -520,6 +513,25 @@ "val" : "https://www.inaturalist.org/observations/47442195" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000025", + "lbl" : "plant gall", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/62135900" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-24T21:38:29Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000026", "lbl" : "faceted", @@ -791,6 +803,19 @@ "val" : "https://www.inaturalist.org/observations/33495996" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "lbl" : "Acraspis erinacei (agamic)", + "type" : "CLASS", + "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" : "2024-03-25T19:27:00Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000040", "lbl" : "nutritive tissue", @@ -824,12 +849,86 @@ "val" : "2024-01-19T02:27:40Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000042", + "lbl" : "Quercus sect. Quercus", + "type" : "CLASS", + "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" : "2024-03-25T01:26:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "lbl" : "Disholcaspis quercusglobulus (sexgen)", + "type" : "CLASS", + "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" : "2024-03-25T01:28:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "lbl" : "Disholcaspis quercusglobulus (agamic)", + "type" : "CLASS", + "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" : "2024-03-25T01:28:48Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "lbl" : "Acraspis erinacei (sexgen)", + "type" : "CLASS", + "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" : "2024-03-25T19:27:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000046", + "lbl" : "Aceria triplacis", + "type" : "CLASS", + "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" : "2024-03-25T19:39:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000047", + "lbl" : "Acraspis gemula", + "type" : "CLASS", + "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" : "2024-03-25T19:40:19Z" + } ] + } } ], "edges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PO_0025496" - }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000002", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PO_0025117" @@ -844,7 +943,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000005", "pred" : "is_a", @@ -933,6 +1032,10 @@ "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000024", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001925" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000025", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025496" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000026", "pred" : "is_a", @@ -964,7 +1067,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000033", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000033", "pred" : "is_a", @@ -984,7 +1087,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000034", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000034", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -992,7 +1095,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000035", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000035", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1000,7 +1103,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000036", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000036", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -1020,7 +1123,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000037", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000037", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -1041,6 +1144,14 @@ "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000038", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PO_0006001" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000040", "pred" : "is_a", @@ -1053,10 +1164,46 @@ "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000041", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000042", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_3511" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000046", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_109362" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000033", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/PO_0025034" @@ -1069,14 +1216,14 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000035", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/PO_0000055" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000036", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/GALLONT_0000009" @@ -1092,7 +1239,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000037", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GALLONT_0000006" diff --git a/gallont-base.obo b/gallont-base.obo index 2eb4a5f..78dff22 100644 --- a/gallont-base.obo +++ b/gallont-base.obo @@ -1,20 +1,18 @@ format-version: 1.2 -data-version: gallont/releases/2024-03-14/gallont-base.owl +data-version: gallont/releases/2024-03-25/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/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 "2024-03-14" xsd:string +property_value: owl:versionInfo "2024-03-25" xsd:string [Term] id: GALLONT:0000001 -name: plant gall -def: "A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism." [] -is_a: PO:0025496 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 -property_value: http://purl.org/dc/terms/date "2023-06-19T19:39:13Z" xsd:string -property_value: seeAlso https://www.inaturalist.org/observations/62135900 +name: DEPRECATED plant gall +comment: Updated the class definition to reflect that this structure is a response to biotic stress +property_value: seeAlso GALLONT:0000025 +is_obsolete: true [Term] id: GALLONT:0000002 @@ -39,7 +37,7 @@ id: GALLONT:0000004 name: kapéllo def: "A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall" [] is_a: PO:0025496 -relationship: BFO:0000050 GALLONT:0000001 ! plant gall +relationship: BFO:0000050 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 "2023-06-22T01:51:19Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/61878883 @@ -240,6 +238,15 @@ property_value: http://purl.org/dc/terms/date "2023-06-26T21:30:22Z" xsd:string property_value: http://purl.org/dc/terms/source https://dictionary.cambridge.org/us/dictionary/english/dimpled property_value: seeAlso https://www.inaturalist.org/observations/47442195 +[Term] +id: GALLONT:0000025 +name: plant gall +def: "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." [] +is_a: PO:0025496 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-24T21:38:29Z" xsd:string +property_value: seeAlso https://www.inaturalist.org/observations/62135900 + [Term] id: GALLONT:0000026 name: faceted @@ -312,9 +319,9 @@ property_value: http://purl.org/dc/terms/date "2023-06-27T01:41:01Z" xsd:string id: GALLONT:0000033 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:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall is_a: UBERON:0001062 -intersection_of: GALLONT:0000001 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: BFO:0000050 PO:0025034 intersection_of: BFO:0000051 PO:0006504 intersection_of: GALLONT:0000000 NCBITaxon:6946 ! has associate @@ -330,7 +337,7 @@ property_value: seeAlso https://www.inaturalist.org/observations/79701805 id: GALLONT:0000034 name: blister gall def: "A plant gall that is part of a leaf and which appears as a portion of swollen tissue, similar to a blister." [] -is_a: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall relationship: BFO:0000050 PO:0025034 property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T22:15:28Z" xsd:string @@ -340,8 +347,8 @@ property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 id: GALLONT:0000035 name: bud gall def: "A plant gall that is located on a bud." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: BFO:0000050 PO:0000055 relationship: BFO:0000050 PO:0000055 property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 @@ -353,8 +360,8 @@ property_value: seeAlso https://www.inaturalist.org/observations/48455720 id: GALLONT:0000036 name: bullet gall def: "A plant gall that is monothalamous and solid, with a shape reminiscent of a bullet. Gall is usually subspherical or subelliptical in shape." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: RO:0000086 GALLONT:0000009 ! monothalamous intersection_of: RO:0000086 GALLONT:0000012 ! solid intersection_of: RO:0000086 GALLONT:0000031 ! semideciduous @@ -372,8 +379,8 @@ property_value: seeAlso https://www.inaturalist.org/observations/58434690 id: GALLONT:0000037 name: roly-poly gall def: "A plant gall that has a detached larval chamber capable of rolling around a hollow chamber located inside the gall." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: BFO:0000051 GALLONT:0000006 ! detached chamber intersection_of: RO:0000086 PATO:0002078 relationship: BFO:0000051 GALLONT:0000006 ! detached chamber @@ -396,6 +403,14 @@ property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: IAO:0000118 "bunch gall" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33495996 +[Term] +id: GALLONT:0000039 +name: Acraspis erinacei (agamic) +is_a: CARO:0000030 +is_a: NCBITaxon:2714064 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:00Z" xsd:dateTime + [Term] id: GALLONT:0000040 name: nutritive tissue @@ -414,6 +429,51 @@ is_a: GALLONT:0000003 ! cavity property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-19T02:27:40Z" xsd:string +[Term] +id: GALLONT:0000042 +name: Quercus sect. Quercus +is_a: NCBITaxon:3511 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:26:41Z" xsd:string + +[Term] +id: GALLONT:0000043 +name: Disholcaspis quercusglobulus (sexgen) +is_a: CARO:0000048 +is_a: NCBITaxon:1540852 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:09Z" xsd:string + +[Term] +id: GALLONT:0000044 +name: Disholcaspis quercusglobulus (agamic) +is_a: CARO:0000030 +is_a: NCBITaxon:1540852 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:48Z" xsd:string + +[Term] +id: GALLONT:0000045 +name: Acraspis erinacei (sexgen) +is_a: CARO:0000048 +is_a: NCBITaxon:2714064 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:17Z" xsd:dateTime + +[Term] +id: GALLONT:0000046 +name: Aceria triplacis +is_a: NCBITaxon:109362 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTime + +[Term] +id: GALLONT:0000047 +name: Acraspis gemula +is_a: NCBITaxon:131567 +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 + [Typedef] id: GALLONT:0000000 name: has associate diff --git a/gallont-base.owl b/gallont-base.owl index 9a96547..b01319e 100644 --- a/gallont-base.owl +++ b/gallont-base.owl @@ -7,15 +7,16 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:dcterms="http://purl.org/dc/terms/"> - + None Plant Gall Ontology - 2024-03-14 + 2024-03-25 @@ -43,6 +44,12 @@ + + + + + + @@ -136,15 +143,25 @@ + + + + + + + + + + + + - - A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism. - - 2023-06-19T19:39:13Z - plant gall - + Updated the class definition to reflect that this structure is a response to biotic stress + DEPRECATED plant gall + + true @@ -182,7 +199,7 @@ - + A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall @@ -480,6 +497,19 @@ + + + + + A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004). + + + 2024-03-24T21:38:29Z + plant gall + + + + @@ -582,7 +612,7 @@ - + @@ -598,7 +628,7 @@ - + @@ -631,7 +661,7 @@ - + @@ -653,7 +683,7 @@ - + @@ -661,7 +691,7 @@ - + @@ -684,7 +714,7 @@ - + @@ -704,7 +734,7 @@ - + @@ -745,7 +775,7 @@ - + @@ -757,7 +787,7 @@ - + @@ -802,6 +832,18 @@ + + + + + + + 2024-03-25T19:27:00Z + Acraspis erinacei (agamic) + + + + @@ -833,6 +875,105 @@ + + + + + + 2024-03-25T01:26:41Z + Quercus sect. Quercus + + + + + + + + + + + 2024-03-25T01:28:09Z + Disholcaspis quercusglobulus (sexgen) + + + + + + + + + + + 2024-03-25T01:28:48Z + Disholcaspis quercusglobulus (agamic) + + + + + + + + + + + 2024-03-25T19:27:17Z + Acraspis erinacei (sexgen) + + + + + + + + + + 2024-03-25T19:39:17Z + Aceria triplacis + + + + + + + + + + 2024-03-25T19:40:19Z + Acraspis gemula + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/gallont-full.json b/gallont-full.json index bdc0863..fb5935c 100644 --- a/gallont-full.json +++ b/gallont-full.json @@ -13,9 +13,9 @@ "val" : "Plant Gall Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-03-14" + "val" : "2024-03-25" } ], - "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-03-14/gallont-full.json" + "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-03-25/gallont-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -474,22 +474,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000001", - "lbl" : "plant gall", + "lbl" : "DEPRECATED plant gall", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism." - }, + "comments" : [ "Updated the class definition to reflect that this structure is a response to biotic stress" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-2119-4663" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-06-19T19:39:13Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.inaturalist.org/observations/62135900" - } ] + "val" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000002", @@ -958,6 +951,25 @@ "val" : "https://www.inaturalist.org/observations/47442195" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000025", + "lbl" : "plant gall", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/62135900" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-24T21:38:29Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000026", "lbl" : "faceted", @@ -1229,6 +1241,19 @@ "val" : "https://www.inaturalist.org/observations/33495996" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "lbl" : "Acraspis erinacei (agamic)", + "type" : "CLASS", + "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" : "2024-03-25T19:27:00Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000040", "lbl" : "nutritive tissue", @@ -1262,6 +1287,84 @@ "val" : "2024-01-19T02:27:40Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000042", + "lbl" : "Quercus sect. 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"http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "pred" : "hasRelatedSynonym", + "val" : "hexapods" + } ], + "xrefs" : [ { + "val" : "GC_ID:1" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "ncbi_taxonomy" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_70320", + "lbl" : "Eriophyidae", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7147", + "lbl" : "Diptera", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_73401", + "lbl" : "Cynipidae", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7399", + "lbl" : "Hymenoptera", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_75144", + "lbl" : "Cynipini", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_88770", + "lbl" : "Panarthropoda", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "GC_ID:1" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "ncbi_taxonomy" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCIT_C48440", "lbl" : "solitary", @@ -12535,10 +12978,6 @@ "sub" : "http://purl.obolibrary.org/obo/FLOPO_0900042", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PO_0025496" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000002", "pred" : "is_a", @@ -12554,7 +12993,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000005", "pred" : "is_a", @@ -12643,6 +13082,10 @@ "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000024", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001925" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000025", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PO_0025496" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000026", "pred" : "is_a", @@ -12674,7 +13117,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000033", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000033", "pred" : "is_a", @@ -12694,7 +13137,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000034", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000034", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -12702,7 +13145,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000035", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000035", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -12710,7 +13153,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000036", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000036", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -12730,7 +13173,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000037", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000001" + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000037", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -12751,6 +13194,14 @@ "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000038", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PO_0006001" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064" }, { "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000040", "pred" : "is_a", @@ -12763,6 +13214,42 @@ "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000041", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000042", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_3511" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000046", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_109362" + }, { + "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/GO_0003674", "pred" : "is_a", @@ -12795,10 +13282,42 @@ "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_109362", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_70320" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1206794", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33317" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_131567", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1389465", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_75144" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1389465" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_75144" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_197562", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_197563" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_197563", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6656" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", "pred" : "is_a", @@ -12807,10 +13326,82 @@ "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33090", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33154", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33154" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33213", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33317", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33406", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7147" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_3503", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_3511", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_3503" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_3513", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000042" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_50557", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6960" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6072", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_88770" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6946", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6960", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_197562" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_70320", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7147", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_73401", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7399" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7399", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_75144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_73401" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_88770", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1206794" }, { "sub" : "http://purl.obolibrary.org/obo/NCIT_C48440", "pred" : "is_a", @@ -15014,7 +15605,7 @@ } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000033", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/PO_0025034" @@ -15027,14 +15618,14 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000035", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/PO_0000055" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000036", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/GALLONT_0000009" @@ -15050,7 +15641,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000037", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GALLONT_0000006" diff --git a/gallont-full.obo b/gallont-full.obo index c261878..e548420 100644 --- a/gallont-full.obo +++ b/gallont-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: gallont/releases/2024-03-14/gallont-full.owl +data-version: gallont/releases/2024-03-25/gallont-full.owl subsetdef: 3_STAR "" subsetdef: abnormal_slim "" subsetdef: absent_slim "" @@ -49,6 +49,7 @@ synonymtypedef: common_name "" synonymtypedef: equivalent_name "" synonymtypedef: genbank_common_name "" synonymtypedef: German "" +synonymtypedef: in_part "" synonymtypedef: Japanese "" synonymtypedef: OMO:0003004 "" synonymtypedef: Spanish "" @@ -57,7 +58,7 @@ ontology: gallont/gallont-full property_value: dcterms-license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/description "None" xsd:string property_value: http://purl.org/dc/terms/title "Plant Gall Ontology" xsd:string -property_value: owl:versionInfo "2024-03-14" xsd:string +property_value: owl:versionInfo "2024-03-25" xsd:string [Term] id: BFO:0000002 @@ -177,12 +178,10 @@ property_value: seeAlso https://www.inaturalist.org/observations/81385187 [Term] id: GALLONT:0000001 -name: plant gall -def: "A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism." [] -is_a: PO:0025496 ! multi-tissue plant structure -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 -property_value: http://purl.org/dc/terms/date "2023-06-19T19:39:13Z" xsd:string -property_value: seeAlso https://www.inaturalist.org/observations/62135900 +name: DEPRECATED plant gall +comment: Updated the class definition to reflect that this structure is a response to biotic stress +property_value: seeAlso GALLONT:0000025 +is_obsolete: true [Term] id: GALLONT:0000002 @@ -207,7 +206,7 @@ id: GALLONT:0000004 name: kapéllo def: "A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall" [] is_a: PO:0025496 ! multi-tissue plant structure -relationship: part_of GALLONT:0000001 ! plant gall +relationship: part_of 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 "2023-06-22T01:51:19Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/61878883 @@ -408,6 +407,15 @@ property_value: http://purl.org/dc/terms/date "2023-06-26T21:30:22Z" xsd:string property_value: http://purl.org/dc/terms/source https://dictionary.cambridge.org/us/dictionary/english/dimpled property_value: seeAlso https://www.inaturalist.org/observations/47442195 +[Term] +id: GALLONT:0000025 +name: plant gall +def: "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." [] +is_a: PO:0025496 ! multi-tissue plant structure +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-24T21:38:29Z" xsd:string +property_value: seeAlso https://www.inaturalist.org/observations/62135900 + [Term] id: GALLONT:0000026 name: faceted @@ -480,9 +488,9 @@ property_value: http://purl.org/dc/terms/date "2023-06-27T01:41:01Z" xsd:string id: GALLONT:0000033 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:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall is_a: UBERON:0001062 ! anatomical entity -intersection_of: GALLONT:0000001 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000000 NCBITaxon:6946 ! has associate Acariformes intersection_of: has_part PO:0006504 ! leaf trichome intersection_of: part_of PO:0025034 ! leaf @@ -498,7 +506,7 @@ property_value: seeAlso https://www.inaturalist.org/observations/79701805 id: GALLONT:0000034 name: blister gall def: "A plant gall that is part of a leaf and which appears as a portion of swollen tissue, similar to a blister." [] -is_a: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall relationship: part_of PO:0025034 ! leaf property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T22:15:28Z" xsd:string @@ -508,8 +516,8 @@ property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 id: GALLONT:0000035 name: bud gall def: "A plant gall that is located on a bud." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: part_of PO:0000055 ! bud relationship: part_of PO:0000055 ! bud property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 @@ -521,8 +529,8 @@ property_value: seeAlso https://www.inaturalist.org/observations/48455720 id: GALLONT:0000036 name: bullet gall def: "A plant gall that is monothalamous and solid, with a shape reminiscent of a bullet. Gall is usually subspherical or subelliptical in shape." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: has_quality GALLONT:0000009 ! monothalamous intersection_of: has_quality GALLONT:0000012 ! solid intersection_of: has_quality GALLONT:0000031 ! semideciduous @@ -540,8 +548,8 @@ property_value: seeAlso https://www.inaturalist.org/observations/58434690 id: GALLONT:0000037 name: roly-poly gall def: "A plant gall that has a detached larval chamber capable of rolling around a hollow chamber located inside the gall." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: has_part GALLONT:0000006 ! detached chamber intersection_of: has_quality PATO:0002078 ! hollow relationship: has_part GALLONT:0000006 ! detached chamber @@ -564,6 +572,14 @@ property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: IAO:0000118 "bunch gall" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33495996 +[Term] +id: GALLONT:0000039 +name: Acraspis erinacei (agamic) +is_a: CARO:0000030 ! asexual organism +is_a: NCBITaxon:2714064 ! Acraspis erinacei +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:00Z" xsd:dateTime + [Term] id: GALLONT:0000040 name: nutritive tissue @@ -582,6 +598,51 @@ is_a: GALLONT:0000003 ! cavity property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-19T02:27:40Z" xsd:string +[Term] +id: GALLONT:0000042 +name: Quercus sect. Quercus +is_a: NCBITaxon:3511 ! Quercus +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:26:41Z" xsd:string + +[Term] +id: GALLONT:0000043 +name: Disholcaspis quercusglobulus (sexgen) +is_a: CARO:0000048 ! gonochoristic organism +is_a: NCBITaxon:1540852 ! Disholcaspis quercusglobulus +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:09Z" xsd:string + +[Term] +id: GALLONT:0000044 +name: Disholcaspis quercusglobulus (agamic) +is_a: CARO:0000030 ! asexual organism +is_a: NCBITaxon:1540852 ! Disholcaspis quercusglobulus +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:48Z" xsd:string + +[Term] +id: GALLONT:0000045 +name: Acraspis erinacei (sexgen) +is_a: CARO:0000048 ! gonochoristic organism +is_a: NCBITaxon:2714064 ! Acraspis erinacei +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:17Z" xsd:dateTime + +[Term] +id: GALLONT:0000046 +name: Aceria triplacis +is_a: NCBITaxon:109362 ! Aceria +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTime + +[Term] +id: GALLONT:0000047 +name: Acraspis gemula +is_a: NCBITaxon:131567 ! cellular organisms +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 + [Term] id: GO:0003674 name: gene product or complex activity @@ -714,6 +775,19 @@ synonym: "all" RELATED synonym [] xref: GC_ID:1 is_a: OBI:0100026 ! organism +[Term] +id: NCBITaxon:109362 +name: Aceria +is_a: NCBITaxon:70320 ! Eriophyidae + +[Term] +id: NCBITaxon:1206794 +name: Ecdysozoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33317 ! Protostomia +property_value: has_rank NCBITaxon:clade + [Term] id: NCBITaxon:131567 name: cellular organisms @@ -722,6 +796,47 @@ synonym: "biota" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1 ! root +[Term] +id: NCBITaxon:1389465 +name: Disholcaspis +is_a: NCBITaxon:75144 ! Cynipini + +[Term] +id: NCBITaxon:1540852 +name: Disholcaspis quercusglobulus +is_a: NCBITaxon:1389465 ! Disholcaspis + +[Term] +id: NCBITaxon:1934078 +name: Acraspis +is_a: NCBITaxon:75144 ! Cynipini + +[Term] +id: NCBITaxon:197562 +name: Pancrustacea +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:10874751 +xref: PMID:11557979 +is_a: NCBITaxon:197563 ! Mandibulata +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:197563 +name: Mandibulata +namespace: ncbi_taxonomy +synonym: "mandibulates" EXACT common_name [] +xref: GC_ID:1 +xref: PMID:11557979 +xref: PMID:9727836 +is_a: NCBITaxon:6656 ! Arthropoda +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:2714064 +name: Acraspis erinacei +is_a: NCBITaxon:1934078 ! Acraspis + [Term] id: NCBITaxon:2759 name: Eukaryota @@ -742,19 +857,156 @@ property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:33090 name: Viridiplantae +namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33317 +name: Protostomia +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33406 +name: Cecidomyiidae +is_a: NCBITaxon:7147 ! Diptera + +[Term] +id: NCBITaxon:3503 +name: Fagaceae +is_a: NCBITaxon:33090 ! Viridiplantae + +[Term] +id: NCBITaxon:3511 +name: Quercus +is_a: NCBITaxon:3503 ! Fagaceae + +[Term] +id: NCBITaxon:3513 +name: Quercus alba +is_a: GALLONT:0000042 ! Quercus sect. Quercus + +[Term] +id: NCBITaxon:50557 +name: Insecta +namespace: ncbi_taxonomy +synonym: "insects" RELATED blast_name [] +synonym: "true insects" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:6960 ! Hexapoda +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:6656 +name: Arthropoda +namespace: ncbi_taxonomy +synonym: "arthropods" EXACT genbank_common_name [] +synonym: "arthropods" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:88770 ! Panarthropoda +property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6946 name: Acariformes is_a: NCBITaxon:2759 ! Eukaryota +[Term] +id: NCBITaxon:6960 +name: Hexapoda +namespace: ncbi_taxonomy +synonym: "Atelocerata" RELATED in_part [] +synonym: "hexapods" RELATED blast_name [] +synonym: "insects" EXACT genbank_common_name [] +synonym: "Tracheata" RELATED in_part [] +synonym: "Uniramia" RELATED in_part [] +xref: GC_ID:1 +is_a: NCBITaxon:197562 ! Pancrustacea +property_value: has_rank NCBITaxon:subphylum + +[Term] +id: NCBITaxon:70320 +name: Eriophyidae +is_a: NCBITaxon:6946 ! Acariformes + +[Term] +id: NCBITaxon:7147 +name: Diptera +is_a: NCBITaxon:50557 ! Insecta + +[Term] +id: NCBITaxon:73401 +name: Cynipidae +is_a: NCBITaxon:7399 ! Hymenoptera + +[Term] +id: NCBITaxon:7399 +name: Hymenoptera +is_a: NCBITaxon:50557 ! Insecta + +[Term] +id: NCBITaxon:75144 +name: Cynipini +is_a: NCBITaxon:73401 ! Cynipidae + +[Term] +id: NCBITaxon:88770 +name: Panarthropoda +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:1206794 ! Ecdysozoa +property_value: has_rank NCBITaxon:clade + [Term] id: NCIT:C48440 name: solitary diff --git a/gallont-full.owl b/gallont-full.owl index 240fe95..41900c0 100644 --- a/gallont-full.owl +++ b/gallont-full.owl @@ -22,11 +22,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + None Plant Gall Ontology - 2024-03-14 + 2024-03-25 @@ -424,6 +424,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -3625,12 +3633,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism. - - 2023-06-19T19:39:13Z - plant gall - + Updated the class definition to reflect that this structure is a response to biotic stress + DEPRECATED plant gall + + true @@ -3668,7 +3674,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall @@ -3966,6 +3972,19 @@ 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 develops in response to a biotic stress (PSO:0000004). + + + 2024-03-24T21:38:29Z + plant gall + + + + @@ -4068,7 +4087,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4084,7 +4103,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4117,7 +4136,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4139,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4147,7 +4166,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4170,7 +4189,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4190,7 +4209,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4231,7 +4250,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4243,7 +4262,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4288,6 +4307,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + 2024-03-25T19:27:00Z + Acraspis erinacei (agamic) + + + + @@ -4319,6 +4350,75 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + 2024-03-25T01:26:41Z + Quercus sect. Quercus + + + + + + + + + + + 2024-03-25T01:28:09Z + Disholcaspis quercusglobulus (sexgen) + + + + + + + + + + + 2024-03-25T01:28:48Z + Disholcaspis quercusglobulus (agamic) + + + + + + + + + + + 2024-03-25T19:27:17Z + Acraspis erinacei (sexgen) + + + + + + + + + + 2024-03-25T19:39:17Z + Aceria triplacis + + + + + + + + + + 2024-03-25T19:40:19Z + Acraspis gemula + + + + @@ -4603,6 +4703,28 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Aceria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1206794 + Ecdysozoa + + + + @@ -4622,6 +4744,79 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Disholcaspis + + + + + + + + + Disholcaspis quercusglobulus + + + + + + + + + Acraspis + + + + + + + + + + GC_ID:1 + PMID:10874751 + PMID:11557979 + ncbi_taxonomy + NCBITaxon:197562 + Pancrustacea + + + + + + + + + + GC_ID:1 + PMID:11557979 + PMID:9727836 + mandibulates + ncbi_taxonomy + NCBITaxon:197563 + Mandibulata + + + + + mandibulates + + + + + + + + + + Acraspis erinacei + + + + @@ -4690,12 +4885,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + GC_ID:1 + PMID:16248873 + PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants + ncbi_taxonomy Chlorobionta Chloroplastida green plants + NCBITaxon:33090 Viridiplantae @@ -4737,6 +4938,203 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + ncbi_taxonomy + Fungi/Metazoa group + opisthokonts + NCBITaxon:33154 + Opisthokonta + + + + + Fungi/Metazoa group + + + + + + opisthokonts + + + + + + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + NCBITaxon:33208 + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33213 + Bilateria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33317 + Protostomia + + + + + + + + + Cecidomyiidae + + + + + + + + + Fagaceae + + + + + + + + + Quercus + + + + + + + + + Quercus alba + + + + + + + + + + GC_ID:1 + true insects + ncbi_taxonomy + insects + NCBITaxon:50557 + Insecta + + + + + true insects + + + + + + insects + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6072 + Eumetazoa + + + + + + + + + + GC_ID:1 + arthropods + ncbi_taxonomy + arthropods + NCBITaxon:6656 + Arthropoda + + + + + arthropods + + + + + + arthropods + + + + + @@ -4746,6 +5144,112 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + insects + ncbi_taxonomy + Atelocerata + Tracheata + Uniramia + hexapods + NCBITaxon:6960 + Hexapoda + + + + + insects + + + + + + Atelocerata + + + + + + Tracheata + + + + + + Uniramia + + + + + + hexapods + + + + + + + + + + Eriophyidae + + + + + + + + + Diptera + + + + + + + + + Cynipidae + + + + + + + + + Hymenoptera + + + + + + + + + Cynipini + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:88770 + Panarthropoda + + + + @@ -13011,7 +13515,7 @@ 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 @@ -13023,14 +13527,14 @@ 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 diff --git a/gallont.json b/gallont.json index 2e37b67..02c35d6 100644 --- a/gallont.json +++ b/gallont.json @@ -13,9 +13,9 @@ "val" : "Plant Gall Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-03-14" + "val" : "2024-03-25" } ], - "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-03-14/gallont.json" + "version" : "http://purl.obolibrary.org/obo/gallont/releases/2024-03-25/gallont.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -474,22 +474,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000001", - "lbl" : "plant gall", + "lbl" : "DEPRECATED plant gall", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism." - }, + "comments" : [ "Updated the class definition to reflect that this structure is a response to biotic stress" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-2119-4663" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-06-19T19:39:13Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.inaturalist.org/observations/62135900" - } ] + "val" : "http://purl.obolibrary.org/obo/GALLONT_0000025" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000002", @@ -958,6 +951,25 @@ "val" : "https://www.inaturalist.org/observations/47442195" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000025", + "lbl" : "plant gall", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/pato#seeAlso", + "val" : "https://www.inaturalist.org/observations/62135900" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-03-24T21:38:29Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000026", "lbl" : "faceted", @@ -1229,6 +1241,19 @@ "val" : "https://www.inaturalist.org/observations/33495996" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000039", + "lbl" : "Acraspis erinacei (agamic)", + "type" : "CLASS", + "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" : "2024-03-25T19:27:00Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GALLONT_0000040", "lbl" : "nutritive tissue", @@ -1262,6 +1287,84 @@ "val" : "2024-01-19T02:27:40Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000042", + "lbl" : "Quercus sect. Quercus", + "type" : "CLASS", + "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" : "2024-03-25T01:26:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "lbl" : "Disholcaspis quercusglobulus (sexgen)", + "type" : "CLASS", + "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" : "2024-03-25T01:28:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "lbl" : "Disholcaspis quercusglobulus (agamic)", + "type" : "CLASS", + "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" : "2024-03-25T01:28:48Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "lbl" : "Acraspis erinacei (sexgen)", + "type" : "CLASS", + "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" : "2024-03-25T19:27:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000046", + "lbl" : "Aceria triplacis", + "type" : "CLASS", + "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" : "2024-03-25T19:39:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GALLONT_0000047", + "lbl" : "Acraspis gemula", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-2119-4663" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/GALLONT_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000042", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_3511" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000043", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000044", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000045", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064" + }, { + "sub" : "http://purl.obolibrary.org/obo/GALLONT_0000046", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_109362" + }, { + "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/GO_0003674", "pred" : "is_a", @@ -12795,10 +13282,42 @@ "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_109362", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_70320" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1206794", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33317" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_131567", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1389465", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_75144" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1540852", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1389465" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_75144" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_197562", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_197563" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_197563", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6656" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2714064", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1934078" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", "pred" : "is_a", @@ -12807,10 +13326,82 @@ "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33090", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33154", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33154" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33213", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33317", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33406", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7147" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_3503", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_3511", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_3503" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_3513", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GALLONT_0000042" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_50557", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6960" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6072", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_88770" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6946", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6960", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_197562" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_70320", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6946" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7147", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_73401", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7399" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7399", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_75144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_73401" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_88770", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1206794" }, { "sub" : "http://purl.obolibrary.org/obo/NCIT_C48440", "pred" : "is_a", @@ -15014,7 +15605,7 @@ } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000033", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/PO_0025034" @@ -15027,14 +15618,14 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000035", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/PO_0000055" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000036", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/GALLONT_0000009" @@ -15050,7 +15641,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GALLONT_0000037", - "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000001" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/GALLONT_0000025" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", "fillerId" : "http://purl.obolibrary.org/obo/GALLONT_0000006" diff --git a/gallont.obo b/gallont.obo index 76298f5..afbe54b 100644 --- a/gallont.obo +++ b/gallont.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-03-14 +data-version: releases/2024-03-25 subsetdef: 3_STAR "" subsetdef: abnormal_slim "" subsetdef: absent_slim "" @@ -49,6 +49,7 @@ synonymtypedef: common_name "" synonymtypedef: equivalent_name "" synonymtypedef: genbank_common_name "" synonymtypedef: German "" +synonymtypedef: in_part "" synonymtypedef: Japanese "" synonymtypedef: OMO:0003004 "" synonymtypedef: Spanish "" @@ -57,7 +58,7 @@ ontology: gallont property_value: dcterms-license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/description "None" xsd:string property_value: http://purl.org/dc/terms/title "Plant Gall Ontology" xsd:string -property_value: owl:versionInfo "2024-03-14" xsd:string +property_value: owl:versionInfo "2024-03-25" xsd:string [Term] id: BFO:0000002 @@ -177,12 +178,10 @@ property_value: seeAlso https://www.inaturalist.org/observations/81385187 [Term] id: GALLONT:0000001 -name: plant gall -def: "A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism." [] -is_a: PO:0025496 ! multi-tissue plant structure -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 -property_value: http://purl.org/dc/terms/date "2023-06-19T19:39:13Z" xsd:string -property_value: seeAlso https://www.inaturalist.org/observations/62135900 +name: DEPRECATED plant gall +comment: Updated the class definition to reflect that this structure is a response to biotic stress +property_value: seeAlso GALLONT:0000025 +is_obsolete: true [Term] id: GALLONT:0000002 @@ -207,7 +206,7 @@ id: GALLONT:0000004 name: kapéllo def: "A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall" [] is_a: PO:0025496 ! multi-tissue plant structure -relationship: part_of GALLONT:0000001 ! plant gall +relationship: part_of 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 "2023-06-22T01:51:19Z" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/61878883 @@ -408,6 +407,15 @@ property_value: http://purl.org/dc/terms/date "2023-06-26T21:30:22Z" xsd:string property_value: http://purl.org/dc/terms/source https://dictionary.cambridge.org/us/dictionary/english/dimpled property_value: seeAlso https://www.inaturalist.org/observations/47442195 +[Term] +id: GALLONT:0000025 +name: plant gall +def: "A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004)." [] +is_a: PO:0025496 ! multi-tissue plant structure +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-24T21:38:29Z" xsd:string +property_value: seeAlso https://www.inaturalist.org/observations/62135900 + [Term] id: GALLONT:0000026 name: faceted @@ -480,9 +488,9 @@ property_value: http://purl.org/dc/terms/date "2023-06-27T01:41:01Z" xsd:string id: GALLONT:0000033 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:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall is_a: UBERON:0001062 ! anatomical entity -intersection_of: GALLONT:0000001 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: GALLONT:0000000 NCBITaxon:6946 ! has associate Acariformes intersection_of: has_part PO:0006504 ! leaf trichome intersection_of: part_of PO:0025034 ! leaf @@ -498,7 +506,7 @@ property_value: seeAlso https://www.inaturalist.org/observations/79701805 id: GALLONT:0000034 name: blister gall def: "A plant gall that is part of a leaf and which appears as a portion of swollen tissue, similar to a blister." [] -is_a: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall relationship: part_of PO:0025034 ! leaf property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2023-08-01T22:15:28Z" xsd:string @@ -508,8 +516,8 @@ property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 id: GALLONT:0000035 name: bud gall def: "A plant gall that is located on a bud." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: part_of PO:0000055 ! bud relationship: part_of PO:0000055 ! bud property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 @@ -521,8 +529,8 @@ property_value: seeAlso https://www.inaturalist.org/observations/48455720 id: GALLONT:0000036 name: bullet gall def: "A plant gall that is monothalamous and solid, with a shape reminiscent of a bullet. Gall is usually subspherical or subelliptical in shape." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: has_quality GALLONT:0000009 ! monothalamous intersection_of: has_quality GALLONT:0000012 ! solid intersection_of: has_quality GALLONT:0000031 ! semideciduous @@ -540,8 +548,8 @@ property_value: seeAlso https://www.inaturalist.org/observations/58434690 id: GALLONT:0000037 name: roly-poly gall def: "A plant gall that has a detached larval chamber capable of rolling around a hollow chamber located inside the gall." [] -is_a: GALLONT:0000001 ! plant gall -intersection_of: GALLONT:0000001 ! plant gall +is_a: GALLONT:0000025 ! plant gall +intersection_of: GALLONT:0000025 ! plant gall intersection_of: has_part GALLONT:0000006 ! detached chamber intersection_of: has_quality PATO:0002078 ! hollow relationship: has_part GALLONT:0000006 ! detached chamber @@ -564,6 +572,14 @@ property_value: http://purl.org/dc/terms/source https://lccn.loc.gov/41001073 property_value: IAO:0000118 "bunch gall" xsd:string property_value: seeAlso https://www.inaturalist.org/observations/33495996 +[Term] +id: GALLONT:0000039 +name: Acraspis erinacei (agamic) +is_a: CARO:0000030 ! asexual organism +is_a: NCBITaxon:2714064 ! Acraspis erinacei +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:00Z" xsd:dateTime + [Term] id: GALLONT:0000040 name: nutritive tissue @@ -582,6 +598,51 @@ is_a: GALLONT:0000003 ! cavity property_value: http://purl.org/dc/terms/creator http://orcid.org/0000-0002-2119-4663 property_value: http://purl.org/dc/terms/date "2024-01-19T02:27:40Z" xsd:string +[Term] +id: GALLONT:0000042 +name: Quercus sect. Quercus +is_a: NCBITaxon:3511 ! Quercus +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:26:41Z" xsd:string + +[Term] +id: GALLONT:0000043 +name: Disholcaspis quercusglobulus (sexgen) +is_a: CARO:0000048 ! gonochoristic organism +is_a: NCBITaxon:1540852 ! Disholcaspis quercusglobulus +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:09Z" xsd:string + +[Term] +id: GALLONT:0000044 +name: Disholcaspis quercusglobulus (agamic) +is_a: CARO:0000030 ! asexual organism +is_a: NCBITaxon:1540852 ! Disholcaspis quercusglobulus +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T01:28:48Z" xsd:string + +[Term] +id: GALLONT:0000045 +name: Acraspis erinacei (sexgen) +is_a: CARO:0000048 ! gonochoristic organism +is_a: NCBITaxon:2714064 ! Acraspis erinacei +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:27:17Z" xsd:dateTime + +[Term] +id: GALLONT:0000046 +name: Aceria triplacis +is_a: NCBITaxon:109362 ! Aceria +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-2119-4663 +property_value: http://purl.org/dc/terms/date "2024-03-25T19:39:17Z" xsd:dateTime + +[Term] +id: GALLONT:0000047 +name: Acraspis gemula +is_a: NCBITaxon:131567 ! cellular organisms +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 + [Term] id: GO:0003674 name: gene product or complex activity @@ -714,6 +775,19 @@ synonym: "all" RELATED synonym [] xref: GC_ID:1 is_a: OBI:0100026 ! organism +[Term] +id: NCBITaxon:109362 +name: Aceria +is_a: NCBITaxon:70320 ! Eriophyidae + +[Term] +id: NCBITaxon:1206794 +name: Ecdysozoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33317 ! Protostomia +property_value: has_rank NCBITaxon:clade + [Term] id: NCBITaxon:131567 name: cellular organisms @@ -722,6 +796,47 @@ synonym: "biota" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1 ! root +[Term] +id: NCBITaxon:1389465 +name: Disholcaspis +is_a: NCBITaxon:75144 ! Cynipini + +[Term] +id: NCBITaxon:1540852 +name: Disholcaspis quercusglobulus +is_a: NCBITaxon:1389465 ! Disholcaspis + +[Term] +id: NCBITaxon:1934078 +name: Acraspis +is_a: NCBITaxon:75144 ! Cynipini + +[Term] +id: NCBITaxon:197562 +name: Pancrustacea +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:10874751 +xref: PMID:11557979 +is_a: NCBITaxon:197563 ! Mandibulata +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:197563 +name: Mandibulata +namespace: ncbi_taxonomy +synonym: "mandibulates" EXACT common_name [] +xref: GC_ID:1 +xref: PMID:11557979 +xref: PMID:9727836 +is_a: NCBITaxon:6656 ! Arthropoda +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:2714064 +name: Acraspis erinacei +is_a: NCBITaxon:1934078 ! Acraspis + [Term] id: NCBITaxon:2759 name: Eukaryota @@ -742,19 +857,156 @@ property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:33090 name: Viridiplantae +namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33317 +name: Protostomia +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:33406 +name: Cecidomyiidae +is_a: NCBITaxon:7147 ! Diptera + +[Term] +id: NCBITaxon:3503 +name: Fagaceae +is_a: NCBITaxon:33090 ! Viridiplantae + +[Term] +id: NCBITaxon:3511 +name: Quercus +is_a: NCBITaxon:3503 ! Fagaceae + +[Term] +id: NCBITaxon:3513 +name: Quercus alba +is_a: GALLONT:0000042 ! Quercus sect. Quercus + +[Term] +id: NCBITaxon:50557 +name: Insecta +namespace: ncbi_taxonomy +synonym: "insects" RELATED blast_name [] +synonym: "true insects" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:6960 ! Hexapoda +property_value: has_rank NCBITaxon:class + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:6656 +name: Arthropoda +namespace: ncbi_taxonomy +synonym: "arthropods" EXACT genbank_common_name [] +synonym: "arthropods" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:88770 ! Panarthropoda +property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6946 name: Acariformes is_a: NCBITaxon:2759 ! Eukaryota +[Term] +id: NCBITaxon:6960 +name: Hexapoda +namespace: ncbi_taxonomy +synonym: "Atelocerata" RELATED in_part [] +synonym: "hexapods" RELATED blast_name [] +synonym: "insects" EXACT genbank_common_name [] +synonym: "Tracheata" RELATED in_part [] +synonym: "Uniramia" RELATED in_part [] +xref: GC_ID:1 +is_a: NCBITaxon:197562 ! Pancrustacea +property_value: has_rank NCBITaxon:subphylum + +[Term] +id: NCBITaxon:70320 +name: Eriophyidae +is_a: NCBITaxon:6946 ! Acariformes + +[Term] +id: NCBITaxon:7147 +name: Diptera +is_a: NCBITaxon:50557 ! Insecta + +[Term] +id: NCBITaxon:73401 +name: Cynipidae +is_a: NCBITaxon:7399 ! Hymenoptera + +[Term] +id: NCBITaxon:7399 +name: Hymenoptera +is_a: NCBITaxon:50557 ! Insecta + +[Term] +id: NCBITaxon:75144 +name: Cynipini +is_a: NCBITaxon:73401 ! Cynipidae + +[Term] +id: NCBITaxon:88770 +name: Panarthropoda +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:1206794 ! Ecdysozoa +property_value: has_rank NCBITaxon:clade + [Term] id: NCIT:C48440 name: solitary diff --git a/gallont.owl b/gallont.owl index 154783d..17154dc 100644 --- a/gallont.owl +++ b/gallont.owl @@ -22,11 +22,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + None Plant Gall Ontology - 2024-03-14 + 2024-03-25 @@ -424,6 +424,14 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + @@ -3625,12 +3633,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - A multi-tissue plant structure, whose development is induced by an organism for the benefit of that organism. - - 2023-06-19T19:39:13Z - plant gall - + Updated the class definition to reflect that this structure is a response to biotic stress + DEPRECATED plant gall + + true @@ -3668,7 +3674,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall @@ -3966,6 +3972,19 @@ 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 develops in response to a biotic stress (PSO:0000004). + + + 2024-03-24T21:38:29Z + plant gall + + + + @@ -4068,7 +4087,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4084,7 +4103,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4117,7 +4136,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4139,7 +4158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4147,7 +4166,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4170,7 +4189,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4190,7 +4209,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4231,7 +4250,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4243,7 +4262,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -4288,6 +4307,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + 2024-03-25T19:27:00Z + Acraspis erinacei (agamic) + + + + @@ -4319,6 +4350,75 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + 2024-03-25T01:26:41Z + Quercus sect. Quercus + + + + + + + + + + + 2024-03-25T01:28:09Z + Disholcaspis quercusglobulus (sexgen) + + + + + + + + + + + 2024-03-25T01:28:48Z + Disholcaspis quercusglobulus (agamic) + + + + + + + + + + + 2024-03-25T19:27:17Z + Acraspis erinacei (sexgen) + + + + + + + + + + 2024-03-25T19:39:17Z + Aceria triplacis + + + + + + + + + + 2024-03-25T19:40:19Z + Acraspis gemula + + + + @@ -4603,6 +4703,28 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Aceria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1206794 + Ecdysozoa + + + + @@ -4622,6 +4744,79 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Disholcaspis + + + + + + + + + Disholcaspis quercusglobulus + + + + + + + + + Acraspis + + + + + + + + + + GC_ID:1 + PMID:10874751 + PMID:11557979 + ncbi_taxonomy + NCBITaxon:197562 + Pancrustacea + + + + + + + + + + GC_ID:1 + PMID:11557979 + PMID:9727836 + mandibulates + ncbi_taxonomy + NCBITaxon:197563 + Mandibulata + + + + + mandibulates + + + + + + + + + + Acraspis erinacei + + + + @@ -4690,12 +4885,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + GC_ID:1 + PMID:16248873 + PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants + ncbi_taxonomy Chlorobionta Chloroplastida green plants + NCBITaxon:33090 Viridiplantae @@ -4737,6 +4938,203 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + ncbi_taxonomy + Fungi/Metazoa group + opisthokonts + NCBITaxon:33154 + Opisthokonta + + + + + Fungi/Metazoa group + + + + + + opisthokonts + + + + + + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + NCBITaxon:33208 + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33213 + Bilateria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33317 + Protostomia + + + + + + + + + Cecidomyiidae + + + + + + + + + Fagaceae + + + + + + + + + Quercus + + + + + + + + + Quercus alba + + + + + + + + + + GC_ID:1 + true insects + ncbi_taxonomy + insects + NCBITaxon:50557 + Insecta + + + + + true insects + + + + + + insects + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6072 + Eumetazoa + + + + + + + + + + GC_ID:1 + arthropods + ncbi_taxonomy + arthropods + NCBITaxon:6656 + Arthropoda + + + + + arthropods + + + + + + arthropods + + + + + @@ -4746,6 +5144,112 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + insects + ncbi_taxonomy + Atelocerata + Tracheata + Uniramia + hexapods + NCBITaxon:6960 + Hexapoda + + + + + insects + + + + + + Atelocerata + + + + + + Tracheata + + + + + + Uniramia + + + + + + hexapods + + + + + + + + + + Eriophyidae + + + + + + + + + Diptera + + + + + + + + + Cynipidae + + + + + + + + + Hymenoptera + + + + + + + + + Cynipini + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:88770 + Panarthropoda + + + + @@ -13011,7 +13515,7 @@ 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 @@ -13023,14 +13527,14 @@ 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 @@ -13932,13 +14436,6 @@ This issue is outside the scope of OBI. Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. multi-tissue plant structure - - - - 複数の組織からなる植物構造 (Japanese, exact) - NIG:Yukiko_Yamazaki - - @@ -13953,6 +14450,13 @@ This issue is outside the scope of OBI. POC:Maria_Alejandra_Gandolfo + + + + 複数の組織からなる植物構造 (Japanese, exact) + NIG:Yukiko_Yamazaki + + diff --git a/src/ontology/gallont-edit.owl b/src/ontology/gallont-edit.owl index f9b95f4..e4453ad 100644 --- a/src/ontology/gallont-edit.owl +++ b/src/ontology/gallont-edit.owl @@ -59,22 +59,31 @@ 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()) +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()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -650,6 +659,14 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (Acraspis erinacei (agamic)) + +AnnotationAssertion(dcterms:creator ) +AnnotationAssertion(dcterms:date "2024-03-25T19:27:00Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Acraspis erinacei (agamic)"@en) +SubClassOf( ) +SubClassOf( ) + # Class: (nutritive tissue) AnnotationAssertion(dcterms:creator ) @@ -691,16 +708,53 @@ AnnotationAssertion(rdfs:label SubClassOf( ) SubClassOf( ) +# Class: (Acraspis erinacei (sexgen)) + +AnnotationAssertion(dcterms:creator ) +AnnotationAssertion(dcterms:date "2024-03-25T19:27:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Acraspis erinacei (sexgen)"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (Aceria triplacis) + +AnnotationAssertion(dcterms:creator ) +AnnotationAssertion(dcterms:date "2024-03-25T19:39:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Aceria triplacis"@en) +SubClassOf( ) + +# Class: (Acraspis gemula) + +AnnotationAssertion(dcterms:creator ) +AnnotationAssertion(dcterms:date "2024-03-25T19:40:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Acraspis gemula"@en) +SubClassOf( ) + +# Class: (Aceria) + +AnnotationAssertion(rdfs:label "Aceria") +SubClassOf( ) + # Class: (Disholcaspis) AnnotationAssertion(rdfs:label "Disholcaspis") -SubClassOf( ) +SubClassOf( ) # Class: (Disholcaspis quercusglobulus) AnnotationAssertion(rdfs:label "Disholcaspis quercusglobulus") SubClassOf( ) +# Class: (Acraspis) + +AnnotationAssertion(rdfs:label "Acraspis") +SubClassOf( ) + +# Class: (Acraspis erinacei) + +AnnotationAssertion(rdfs:label "Acraspis erinacei") +SubClassOf( ) + # Class: (Cecidomyiidae) AnnotationAssertion(rdfs:label "Cecidomyiidae") @@ -731,6 +785,11 @@ SubClassOf( "Acariformes"@en) SubClassOf( ) +# Class: (Eriophyidae) + +AnnotationAssertion(rdfs:label "Eriophyidae") +SubClassOf( ) + # Class: (Diptera) AnnotationAssertion(rdfs:label "Diptera") @@ -746,6 +805,11 @@ SubClassOf( "Hymenoptera") SubClassOf( ) +# Class: (Cynipini) + +AnnotationAssertion(rdfs:label "Cynipini") +SubClassOf( ) + # Class: (solitary) AnnotationAssertion( "Not accompanied by another or others; exclusive of anyone or anything else."@en) diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index 60e5131..13beb34 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 "2024-03-14") +Annotation(owl:versionInfo "2024-03-25") Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 19d3654..ef112df 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 "2024-03-14") +Annotation(owl:versionInfo "2024-03-25") Declaration(Class()) Declaration(Class()) @@ -30,8 +30,21 @@ 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()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -339,8 +352,10 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -488,10 +503,18 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -2156,6 +2179,15 @@ AnnotationAssertion( "root") SubClassOf( ) +# Class: (Ecdysozoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:1206794") +AnnotationAssertion(rdfs:label "Ecdysozoa") +SubClassOf( ) + # Class: (cellular organisms) AnnotationAssertion( "GC_ID:1") @@ -2165,6 +2197,29 @@ AnnotationAssertion( "cellular organisms") SubClassOf( ) +# Class: (Pancrustacea) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:10874751") +AnnotationAssertion( "PMID:11557979") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:197562") +AnnotationAssertion(rdfs:label "Pancrustacea") +SubClassOf( ) + +# Class: (Mandibulata) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:11557979") +AnnotationAssertion( "PMID:9727836") +AnnotationAssertion(Annotation( ) "mandibulates") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:197563") +AnnotationAssertion(rdfs:label "Mandibulata") +SubClassOf( ) + # Class: (Eukaryota) AnnotationAssertion( ) @@ -2183,6 +2238,119 @@ AnnotationAssertion( "Eukaryota") SubClassOf( ) +# Class: (Viridiplantae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:16248873") +AnnotationAssertion( "PMID:30257078") +AnnotationAssertion(Annotation( ) "Chlorophyta/Embryophyta group") +AnnotationAssertion(Annotation( ) "chlorophyte/embryophyte group") +AnnotationAssertion(Annotation( ) "green plants") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Chlorobionta") +AnnotationAssertion(Annotation( ) "Chloroplastida") +AnnotationAssertion(Annotation( ) "green plants") +AnnotationAssertion( "NCBITaxon:33090") +AnnotationAssertion(rdfs:label "Viridiplantae") +SubClassOf( ) + +# Class: (Opisthokonta) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Fungi/Metazoa group") +AnnotationAssertion(Annotation( ) "opisthokonts") +AnnotationAssertion( "NCBITaxon:33154") +AnnotationAssertion(rdfs:label "Opisthokonta") +SubClassOf( ) + +# Class: (Metazoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "metazoans") +AnnotationAssertion(Annotation( ) "multicellular animals") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Animalia") +AnnotationAssertion(Annotation( ) "animals") +AnnotationAssertion( "NCBITaxon:33208") +AnnotationAssertion(rdfs:label "Metazoa") +SubClassOf( ) + +# Class: (Bilateria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33213") +AnnotationAssertion(rdfs:label "Bilateria") +SubClassOf( ) + +# Class: (Protostomia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33317") +AnnotationAssertion(rdfs:label "Protostomia") +SubClassOf( ) + +# Class: (Insecta) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "true insects") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "insects") +AnnotationAssertion( "NCBITaxon:50557") +AnnotationAssertion(rdfs:label "Insecta") +SubClassOf( ) + +# Class: (Eumetazoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6072") +AnnotationAssertion(rdfs:label "Eumetazoa") +SubClassOf( ) + +# Class: (Arthropoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "arthropods") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "arthropods") +AnnotationAssertion( "NCBITaxon:6656") +AnnotationAssertion(rdfs:label "Arthropoda") +SubClassOf( ) + +# Class: (Hexapoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "insects") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Atelocerata") +AnnotationAssertion(Annotation( ) "Tracheata") +AnnotationAssertion(Annotation( ) "Uniramia") +AnnotationAssertion(Annotation( ) "hexapods") +AnnotationAssertion( "NCBITaxon:6960") +AnnotationAssertion(rdfs:label "Hexapoda") +SubClassOf( ) + +# Class: (Panarthropoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:88770") +AnnotationAssertion(rdfs:label "Panarthropoda") +SubClassOf( ) + # Class: (quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") diff --git a/src/ontology/imports/po_import.owl b/src/ontology/imports/po_import.owl index b188c44..b7c516e 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 "2024-03-14") +Annotation(owl:versionInfo "2024-03-25") Declaration(Class()) Declaration(Class()) @@ -456,7 +456,7 @@ 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") @@ -469,7 +469,7 @@ SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (has part) +# Object Property: (has_part) AnnotationAssertion( "a core relation that holds between a whole and its part"@en) AnnotationAssertion( "BFO:0000051") @@ -481,10 +481,10 @@ AnnotationAssertion(rdfs:label "has 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") @@ -509,8 +509,8 @@ AnnotationAssertion( "plant_ontology") AnnotationAssertion( "precedes") AnnotationAssertion( "precedes") -AnnotationAssertion(rdfs:label "precedes") AnnotationAssertion(rdfs:label "precedes"@en) +AnnotationAssertion(rdfs:label "precedes") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -524,7 +524,7 @@ SubObjectPropertyOf( ) FunctionalObjectProperty() -# Object Property: (bearer of) +# Object Property: (has characteristic) AnnotationAssertion( "Inverse of characteristic_of"@en) AnnotationAssertion(rdfs:label "has characteristic"@en) @@ -544,7 +544,7 @@ 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") @@ -1964,7 +1964,7 @@ 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)") @@ -1976,7 +1976,7 @@ 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)") @@ -2505,6 +2505,7 @@ 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( )) @@ -2639,7 +2640,7 @@ 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") @@ -3618,10 +3619,10 @@ 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(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()))) @@ -3630,17 +3631,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V 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()))) +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 8db9adb..c8701bf 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 "2024-03-14") +Annotation(owl:versionInfo "2024-03-25") Declaration(Class()) Declaration(Class())