diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index ec0efec..7ed9cc4 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5.2 + container: obolibrary/odkfull:v1.5.4 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/imports/merged_import.owl b/imports/merged_import.owl index ae0ff74..81d1dd1 100644 --- a/imports/merged_import.owl +++ b/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-10-29") + +Annotation(owl:versionInfo "2025-01-10") Declaration(Class()) Declaration(Class()) @@ -47,12 +47,19 @@ 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()) @@ -60,6 +67,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -702,14 +710,14 @@ SubClassOf( (specimen role) -AnnotationAssertion( "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en) +AnnotationAssertion( "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen."@en) AnnotationAssertion(rdfs:label "specimen role"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (specimen collection process) -AnnotationAssertion( "A planned process with the objective of collecting a specimen."@en) +AnnotationAssertion( "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed."@en) AnnotationAssertion(rdfs:label "specimen collection process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -718,10 +726,17 @@ SubClassOf( ObjectSomeValuesFrom( (specimen collection objective) -AnnotationAssertion( "A objective specification to obtain a material entity for potential use as an input during an investigation."@en) +AnnotationAssertion( "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed."@en) AnnotationAssertion(rdfs:label "specimen collection objective") SubClassOf( ) +# Class: (specimen from organism) + +AnnotationAssertion( "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)."@en) +AnnotationAssertion(rdfs:label "specimen from organism") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))))) +SubClassOf( ) + # Class: (collection of specimens) AnnotationAssertion( "A material entity that has two or more specimens as its parts."@en) @@ -729,9 +744,23 @@ AnnotationAssertion(rdfs:label "col EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) SubClassOf( ) +# Class: (individual organism specimen) + +AnnotationAssertion( "A specimen composed of an individual organism to be studied in an investigation."@en) +AnnotationAssertion(rdfs:label "individual organism specimen") +EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion(rdfs:label "organism"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + # Class: (specimen) -AnnotationAssertion( "A material entity that has the specimen role."@en) +AnnotationAssertion( "A material entity that is collected for potential use as an input upon which measurements or observations are performed."@en) AnnotationAssertion(rdfs:label "specimen"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 7f18799..6a6be40 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for vfbext # Generated using ontology-development-kit -# ODK Version: v1.5.2 +# ODK Version: v1.5.4 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead @@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.5.2 +ODK_VERSION_MAKEFILE = v1.5.4 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index ae0ff74..81d1dd1 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-10-29") + +Annotation(owl:versionInfo "2025-01-10") Declaration(Class()) Declaration(Class()) @@ -47,12 +47,19 @@ 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()) @@ -60,6 +67,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -702,14 +710,14 @@ SubClassOf( (specimen role) -AnnotationAssertion( "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en) +AnnotationAssertion( "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen."@en) AnnotationAssertion(rdfs:label "specimen role"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (specimen collection process) -AnnotationAssertion( "A planned process with the objective of collecting a specimen."@en) +AnnotationAssertion( "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed."@en) AnnotationAssertion(rdfs:label "specimen collection process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -718,10 +726,17 @@ SubClassOf( ObjectSomeValuesFrom( (specimen collection objective) -AnnotationAssertion( "A objective specification to obtain a material entity for potential use as an input during an investigation."@en) +AnnotationAssertion( "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed."@en) AnnotationAssertion(rdfs:label "specimen collection objective") SubClassOf( ) +# Class: (specimen from organism) + +AnnotationAssertion( "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)."@en) +AnnotationAssertion(rdfs:label "specimen from organism") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))))) +SubClassOf( ) + # Class: (collection of specimens) AnnotationAssertion( "A material entity that has two or more specimens as its parts."@en) @@ -729,9 +744,23 @@ AnnotationAssertion(rdfs:label "col EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) SubClassOf( ) +# Class: (individual organism specimen) + +AnnotationAssertion( "A specimen composed of an individual organism to be studied in an investigation."@en) +AnnotationAssertion(rdfs:label "individual organism specimen") +EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion(rdfs:label "organism"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + # Class: (specimen) -AnnotationAssertion( "A material entity that has the specimen role."@en) +AnnotationAssertion( "A material entity that is collected for potential use as an input upon which measurements or observations are performed."@en) AnnotationAssertion(rdfs:label "specimen"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index c329b0b..3bedab0 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -1,8 +1,8 @@ ?cls ?def ?xrefs "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." - "A objective specification to obtain a material entity for potential use as an input during an investigation."@en "An individual member of a clade of cellular organisms." + "An anatomical structure that has more than one cell as a part." "Anatomical entity that has no mass." "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " @@ -10,22 +10,26 @@ "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." - "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en "A process that realizes a plan which is the concretization of a plan specification."@en "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument."@en + "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen."@en "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." "An anatomical structure that has no cells or cell parts as a part." + "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)."@en "An anatomical entity that has mass." + "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." "CL:0000000 GO:0005623" + "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed."@en "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." + "A material entity that is collected for potential use as an input upon which measurements or observations are performed."@en "Anatomical entity which is part_of Drosophila melanogaster." "UBERON:0001062" "A material entity that has two or more specimens as its parts."@en @@ -36,24 +40,28 @@ + "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." - "A planned process with the objective of collecting a specimen."@en + "A specimen composed of an individual organism to be studied in an investigation."@en "An anatomical structure consisting of one or more cells." "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." "Anatomical structure that has multiple cells as parts." "UBERON:0010000" "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." "UBERON:0000061 CARO:0000003" + + - "A material entity that has the specimen role."@en "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." + "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en "UBERON:0000465 CARO:0000006" + "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed."@en diff --git a/src/ontology/reports/class-count-by-prefix.tsv b/src/ontology/reports/class-count-by-prefix.tsv index 5d78978..a787d88 100644 --- a/src/ontology/reports/class-count-by-prefix.tsv +++ b/src/ontology/reports/class-count-by-prefix.tsv @@ -1,13 +1,13 @@ ?prefix ?numberOfClasses -"OBI" 6 +"OBI" 9 "CARO" 20 "FBbt" 4 "IAO" 2 "BFO" 11 "fbbt/vfb/VFBext" 5 -"NCBITaxon" 1 +"NCBITaxon" 5 "fbbt/vfb/VFB" 1 "SO" 1 -"UBERON" 1 +"UBERON" 2 "PATO" 5 "" 1 diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv index 8c86767..2f0b00e 100644 --- a/src/ontology/reports/edges.tsv +++ b/src/ontology/reports/edges.tsv @@ -1,17 +1,17 @@ ?x ?p ?y - _:B64606b31X2Dbb81X2D4a28X2D9335X2D0b6c5cdcc722genid103 - - - + - - - - - + + + _:B3ef6d6abX2Df3e4X2D4fdaX2Dbd96X2Ddb39520aa73bgenid103 + + + + + @@ -31,6 +31,7 @@ + _:B3ef6d6abX2Df3e4X2D4fdaX2Dbd96X2Ddb39520aa73bgenid62 @@ -45,11 +46,11 @@ - _:B64606b31X2Dbb81X2D4a28X2D9335X2D0b6c5cdcc722genid62 + @@ -57,10 +58,12 @@ + + diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv index 3d94180..c2e7e3f 100644 --- a/src/ontology/reports/synonyms.tsv +++ b/src/ontology/reports/synonyms.tsv @@ -5,6 +5,7 @@ "multi channel image" "expression pattern fragment"@en "cell cluster" + "individual organism specimen" "acellular anatomical structure" "specimen role"@en "immaterial entity"@en @@ -42,6 +43,8 @@ "organism substance" "organism" "role"@en + "organism"@en + "specimen from organism" "specimen collection objective" "collection of specimens"@en "gross anatomical part"@en diff --git a/vfbext-base.json b/vfbext-base.json index 7294736..d6b22a3 100644 --- a/vfbext-base.json +++ b/vfbext-base.json @@ -16,15 +16,15 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "29:10:2024 10:21" + "val" : "10:01:2025 10:50" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-10-29" + "val" : "2025-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-10-29/vfbext-base.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2025-01-10/vfbext-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", diff --git a/vfbext-base.obo b/vfbext-base.obo index 069ba00..8f590b2 100644 --- a/vfbext-base.obo +++ b/vfbext-base.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-10-29/vfbext-base.owl -date: 29:10:2024 10:21 +data-version: vfbext/releases/2025-01-10/vfbext-base.owl +date: 10:01:2025 10:50 idspace: dc http://purl.org/dc/elements/1.1/ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: terms http://purl.org/dc/terms/ @@ -9,7 +9,7 @@ ontology: vfbext/vfbext-base property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: dc:title "VFB Extension Ontology" xsd:string property_value: dc:type IAO:8000001 -property_value: owl:versionInfo "2024-10-29" xsd:string +property_value: owl:versionInfo "2025-01-10" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] diff --git a/vfbext-base.owl b/vfbext-base.owl index 43792e5..d360c24 100644 --- a/vfbext-base.owl +++ b/vfbext-base.owl @@ -13,14 +13,14 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 29:10:2024 10:21 + 10:01:2025 10:50 VFB extension ontology - 2024-10-29 + 2025-01-10 diff --git a/vfbext-full.json b/vfbext-full.json index 1a52bd6..e29017e 100644 --- a/vfbext-full.json +++ b/vfbext-full.json @@ -13,15 +13,15 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "29:10:2024 10:21" + "val" : "10:01:2025 10:49" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-10-29" + "val" : "2025-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-10-29/vfbext-full.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2025-01-10/vfbext-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000001", @@ -330,6 +330,18 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000104", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", "type" : "CLASS" @@ -348,7 +360,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" + "val" : "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." } } }, { @@ -357,7 +369,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process with the objective of collecting a specimen." + "val" : "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." } } }, { @@ -366,7 +378,16 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A objective specification to obtain a material entity for potential use as an input during an investigation." + "val" : "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001479", + "lbl" : "specimen from organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." } } }, { @@ -378,13 +399,31 @@ "val" : "A material entity that has two or more specimens as its parts." } } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0002648", + "lbl" : "individual organism specimen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specimen composed of an individual organism to be studied in an investigation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "lbl" : "organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." + } + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100051", "lbl" : "specimen", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that has the specimen role." + "val" : "A material entity that is collected for potential use as an input upon which measurements or observations are performed." } } }, { @@ -408,6 +447,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "lbl" : "cell cluster", @@ -1184,6 +1226,22 @@ "sub" : "http://purl.obolibrary.org/obo/FBbt_10000000", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", @@ -1212,10 +1270,26 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000684", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0001479", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0002076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0002648", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0002648", + "pred" : "http://purl.obolibrary.org/obo/RO_0002180", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", "pred" : "is_a", @@ -1420,6 +1494,9 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000417", "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000684" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0001479", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100051" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0100051", "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], diff --git a/vfbext-full.obo b/vfbext-full.obo index 4767975..d08103a 100644 --- a/vfbext-full.obo +++ b/vfbext-full.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-10-29/vfbext-full.owl -date: 29:10:2024 10:21 +data-version: vfbext/releases/2025-01-10/vfbext-full.owl +date: 10:01:2025 10:49 subsetdef: clone "" subsetdef: core "" subsetdef: cur "" @@ -24,7 +24,7 @@ remark: VFB extension ontology ontology: vfbext/vfbext-full property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: dc:title "VFB Extension Ontology" xsd:string -property_value: owl:versionInfo "2024-10-29" xsd:string +property_value: owl:versionInfo "2025-01-10" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] @@ -307,6 +307,22 @@ intersection_of: CARO:0000000 ! anatomical entity intersection_of: BFO:0000050 NCBITaxon:7227 ! part of relationship: BFO:0000050 NCBITaxon:7227 ! part of +[Term] +id: NCBITaxon:10239 +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:2 +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:2157 +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:2759 +is_a: OBI:0100026 ! organism + [Term] id: OBI:0000011 name: planned process @@ -316,13 +332,13 @@ is_a: BFO:0000015 ! process [Term] id: OBI:0000112 name: specimen role -def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +def: "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000659 name: specimen collection process -def: "A planned process with the objective of collecting a specimen." [] +def: "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective @@ -333,9 +349,15 @@ relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen coll [Term] id: OBI:0000684 name: specimen collection objective -def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +def: "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: IAO:0000005 +[Term] +id: OBI:0001479 +name: specimen from organism +def: "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." [] +is_a: OBI:0100051 ! specimen + [Term] id: OBI:0002076 name: collection of specimens @@ -344,10 +366,29 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen +[Term] +id: OBI:0002648 +name: individual organism specimen +def: "A specimen composed of an individual organism to be studied in an investigation." [] +is_a: OBI:0100051 ! specimen +intersection_of: OBI:0100051 ! specimen +intersection_of: RO:0002180 OBI:0100026 {cardinality="1"} ! has component organism +relationship: RO:0002180 OBI:0100026 ! has component organism + +[Term] +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity +union_of: NCBITaxon:10239 +union_of: NCBITaxon:2 +union_of: NCBITaxon:2157 +union_of: NCBITaxon:2759 + [Term] id: OBI:0100051 name: specimen -def: "A material entity that has the specimen role." [] +def: "A material entity that is collected for potential use as an input upon which measurements or observations are performed." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role diff --git a/vfbext-full.owl b/vfbext-full.owl index d351060..37c48b5 100644 --- a/vfbext-full.owl +++ b/vfbext-full.owl @@ -17,13 +17,13 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 29:10:2024 10:21 + 10:01:2025 10:49 VFB extension ontology - 2024-10-29 + 2025-01-10 @@ -1493,6 +1493,38 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1551,7 +1583,7 @@ Examples include: the relationship between two channels collected simultaneously - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. specimen role @@ -1590,7 +1622,7 @@ Examples include: the relationship between two channels collected simultaneously - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. specimen collection process @@ -1600,12 +1632,75 @@ Examples include: the relationship between two channels collected simultaneously - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. specimen collection objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + specimen from organism + + + + @@ -1627,6 +1722,54 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + 1 + + + + + + + + + + + + + A specimen composed of an individual organism to be studied in an investigation. + individual organism specimen + + + + + + + + + + + + + + + + + + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + organism + + + + @@ -1648,7 +1791,7 @@ Examples include: the relationship between two channels collected simultaneously - A material entity that has the specimen role. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. specimen @@ -1698,6 +1841,12 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + diff --git a/vfbext-non-classified.json b/vfbext-non-classified.json index 732d7ad..718ddb0 100644 --- a/vfbext-non-classified.json +++ b/vfbext-non-classified.json @@ -13,15 +13,15 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "29:10:2024 10:21" + "val" : "10:01:2025 10:50" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-10-29" + "val" : "2025-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-10-29/vfbext-non-classified.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2025-01-10/vfbext-non-classified.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000001", @@ -330,6 +330,18 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000104", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", "type" : "CLASS" @@ -348,7 +360,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" + "val" : "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." } } }, { @@ -357,7 +369,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process with the objective of collecting a specimen." + "val" : "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." } } }, { @@ -366,7 +378,16 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A objective specification to obtain a material entity for potential use as an input during an investigation." + "val" : "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001479", + "lbl" : "specimen from organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." } } }, { @@ -378,13 +399,31 @@ "val" : "A material entity that has two or more specimens as its parts." } } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0002648", + "lbl" : "individual organism specimen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specimen composed of an individual organism to be studied in an investigation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "lbl" : "organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." + } + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100051", "lbl" : "specimen", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that has the specimen role." + "val" : "A material entity that is collected for potential use as an input upon which measurements or observations are performed." } } }, { @@ -408,6 +447,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "lbl" : "cell cluster", @@ -1208,10 +1250,22 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000684", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0001479", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0002076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0002648", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", "pred" : "is_a", @@ -1404,6 +1458,9 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000417", "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000684" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0001479", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100051" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0100051", "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], diff --git a/vfbext-non-classified.obo b/vfbext-non-classified.obo index e004ee1..aed2ae5 100644 --- a/vfbext-non-classified.obo +++ b/vfbext-non-classified.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-10-29/vfbext-non-classified.owl -date: 29:10:2024 10:21 +data-version: vfbext/releases/2025-01-10/vfbext-non-classified.owl +date: 10:01:2025 10:50 subsetdef: clone "" subsetdef: core "" subsetdef: cur "" @@ -24,7 +24,7 @@ remark: VFB extension ontology ontology: vfbext/vfbext-non-classified property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: dc:title "VFB Extension Ontology" xsd:string -property_value: owl:versionInfo "2024-10-29" xsd:string +property_value: owl:versionInfo "2025-01-10" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] @@ -316,13 +316,13 @@ is_a: BFO:0000015 ! process [Term] id: OBI:0000112 name: specimen role -def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +def: "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000659 name: specimen collection process -def: "A planned process with the objective of collecting a specimen." [] +def: "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective @@ -332,9 +332,15 @@ relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen [Term] id: OBI:0000684 name: specimen collection objective -def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +def: "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: IAO:0000005 +[Term] +id: OBI:0001479 +name: specimen from organism +def: "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." [] +is_a: OBI:0100051 ! specimen + [Term] id: OBI:0002076 name: collection of specimens @@ -343,10 +349,28 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen +[Term] +id: OBI:0002648 +name: individual organism specimen +def: "A specimen composed of an individual organism to be studied in an investigation." [] +is_a: OBI:0100051 ! specimen +intersection_of: OBI:0100051 ! specimen +intersection_of: RO:0002180 OBI:0100026 {cardinality="1"} ! has component organism + +[Term] +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity +union_of: NCBITaxon:10239 +union_of: NCBITaxon:2 +union_of: NCBITaxon:2157 +union_of: NCBITaxon:2759 + [Term] id: OBI:0100051 name: specimen -def: "A material entity that has the specimen role." [] +def: "A material entity that is collected for potential use as an input upon which measurements or observations are performed." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role diff --git a/vfbext-non-classified.owl b/vfbext-non-classified.owl index 2621dea..ca037b6 100644 --- a/vfbext-non-classified.owl +++ b/vfbext-non-classified.owl @@ -17,13 +17,13 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 29:10:2024 10:21 + 10:01:2025 10:50 VFB extension ontology - 2024-10-29 + 2025-01-10 @@ -1493,6 +1493,30 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + + @@ -1540,7 +1564,7 @@ Examples include: the relationship between two channels collected simultaneously - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. specimen role @@ -1573,7 +1597,7 @@ Examples include: the relationship between two channels collected simultaneously - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. specimen collection process @@ -1583,12 +1607,51 @@ Examples include: the relationship between two channels collected simultaneously - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. specimen collection objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + specimen from organism + + + + @@ -1610,6 +1673,48 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + 1 + + + + + + + A specimen composed of an individual organism to be studied in an investigation. + individual organism specimen + + + + + + + + + + + + + + + + + + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + organism + + + + @@ -1625,7 +1730,7 @@ Examples include: the relationship between two channels collected simultaneously - A material entity that has the specimen role. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. specimen @@ -1675,6 +1780,12 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + diff --git a/vfbext-simple.json b/vfbext-simple.json index aef3625..c976ecb 100644 --- a/vfbext-simple.json +++ b/vfbext-simple.json @@ -13,15 +13,15 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "29:10:2024 10:21" + "val" : "10:01:2025 10:50" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-10-29" + "val" : "2025-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-10-29/vfbext-simple.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2025-01-10/vfbext-simple.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", diff --git a/vfbext-simple.obo b/vfbext-simple.obo index fb54e07..0f264eb 100644 --- a/vfbext-simple.obo +++ b/vfbext-simple.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2024-10-29/vfbext-simple.owl -date: 29:10:2024 10:21 +data-version: vfbext/releases/2025-01-10/vfbext-simple.owl +date: 10:01:2025 10:50 subsetdef: clone "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -17,7 +17,7 @@ remark: VFB extension ontology ontology: vfbext/vfbext-simple property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: dc:title "VFB Extension Ontology" xsd:string -property_value: owl:versionInfo "2024-10-29" xsd:string +property_value: owl:versionInfo "2025-01-10" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] diff --git a/vfbext-simple.owl b/vfbext-simple.owl index 9981827..e001b60 100644 --- a/vfbext-simple.owl +++ b/vfbext-simple.owl @@ -13,13 +13,13 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 29:10:2024 10:21 + 10:01:2025 10:50 VFB extension ontology - 2024-10-29 + 2025-01-10 diff --git a/vfbext.json b/vfbext.json index dbd57a2..4ba9fd5 100644 --- a/vfbext.json +++ b/vfbext.json @@ -13,15 +13,15 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "29:10:2024 10:21" + "val" : "10:01:2025 10:49" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-10-29" + "val" : "2025-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2024-10-29/vfbext.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2025-01-10/vfbext.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000001", @@ -330,6 +330,18 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000104", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", "type" : "CLASS" @@ -348,7 +360,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" + "val" : "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." } } }, { @@ -357,7 +369,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process with the objective of collecting a specimen." + "val" : "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." } } }, { @@ -366,7 +378,16 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A objective specification to obtain a material entity for potential use as an input during an investigation." + "val" : "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001479", + "lbl" : "specimen from organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." } } }, { @@ -378,13 +399,31 @@ "val" : "A material entity that has two or more specimens as its parts." } } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0002648", + "lbl" : "individual organism specimen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specimen composed of an individual organism to be studied in an investigation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "lbl" : "organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." + } + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100051", "lbl" : "specimen", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that has the specimen role." + "val" : "A material entity that is collected for potential use as an input upon which measurements or observations are performed." } } }, { @@ -408,6 +447,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "lbl" : "cell cluster", @@ -1184,6 +1226,22 @@ "sub" : "http://purl.obolibrary.org/obo/FBbt_10000000", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", @@ -1212,10 +1270,26 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000684", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0001479", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0002076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0002648", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0002648", + "pred" : "http://purl.obolibrary.org/obo/RO_0002180", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", "pred" : "is_a", @@ -1420,6 +1494,9 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000417", "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000684" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0001479", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100051" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0100051", "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], diff --git a/vfbext.obo b/vfbext.obo index 4de2eaf..595183b 100644 --- a/vfbext.obo +++ b/vfbext.obo @@ -1,5 +1,5 @@ format-version: 1.2 -date: 29:10:2024 10:21 +date: 10:01:2025 10:49 subsetdef: clone "" subsetdef: core "" subsetdef: cur "" @@ -23,7 +23,7 @@ remark: VFB extension ontology ontology: http://virtualflybrain.org/data/VFB/OWL/vfbext.owl property_value: dc:description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: dc:title "VFB Extension Ontology" xsd:string -property_value: owl:versionInfo "2024-10-29" xsd:string +property_value: owl:versionInfo "2025-01-10" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] @@ -306,6 +306,22 @@ intersection_of: CARO:0000000 ! anatomical entity intersection_of: BFO:0000050 NCBITaxon:7227 ! part of relationship: BFO:0000050 NCBITaxon:7227 ! part of +[Term] +id: NCBITaxon:10239 +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:2 +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:2157 +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:2759 +is_a: OBI:0100026 ! organism + [Term] id: OBI:0000011 name: planned process @@ -315,13 +331,13 @@ is_a: BFO:0000015 ! process [Term] id: OBI:0000112 name: specimen role -def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +def: "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000659 name: specimen collection process -def: "A planned process with the objective of collecting a specimen." [] +def: "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective @@ -332,9 +348,15 @@ relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen coll [Term] id: OBI:0000684 name: specimen collection objective -def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +def: "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: IAO:0000005 +[Term] +id: OBI:0001479 +name: specimen from organism +def: "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." [] +is_a: OBI:0100051 ! specimen + [Term] id: OBI:0002076 name: collection of specimens @@ -343,10 +365,29 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen +[Term] +id: OBI:0002648 +name: individual organism specimen +def: "A specimen composed of an individual organism to be studied in an investigation." [] +is_a: OBI:0100051 ! specimen +intersection_of: OBI:0100051 ! specimen +intersection_of: RO:0002180 OBI:0100026 {cardinality="1"} ! has component organism +relationship: RO:0002180 OBI:0100026 ! has component organism + +[Term] +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity +union_of: NCBITaxon:10239 +union_of: NCBITaxon:2 +union_of: NCBITaxon:2157 +union_of: NCBITaxon:2759 + [Term] id: OBI:0100051 name: specimen -def: "A material entity that has the specimen role." [] +def: "A material entity that is collected for potential use as an input upon which measurements or observations are performed." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role diff --git a/vfbext.owl b/vfbext.owl index a3707b7..8e72626 100644 --- a/vfbext.owl +++ b/vfbext.owl @@ -20,9 +20,9 @@ An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 29:10:2024 10:21 + 10:01:2025 10:49 VFB extension ontology - 2024-10-29 + 2025-01-10 @@ -1492,6 +1492,38 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1550,7 +1582,7 @@ Examples include: the relationship between two channels collected simultaneously - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. specimen role @@ -1589,7 +1621,7 @@ Examples include: the relationship between two channels collected simultaneously - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. specimen collection process @@ -1599,12 +1631,75 @@ Examples include: the relationship between two channels collected simultaneously - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. specimen collection objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + specimen from organism + + + + @@ -1626,6 +1721,54 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + 1 + + + + + + + + + + + + + A specimen composed of an individual organism to be studied in an investigation. + individual organism specimen + + + + + + + + + + + + + + + + + + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + organism + + + + @@ -1647,7 +1790,7 @@ Examples include: the relationship between two channels collected simultaneously - A material entity that has the specimen role. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. specimen @@ -1697,6 +1840,12 @@ Examples include: the relationship between two channels collected simultaneously + + + + + +