diff --git a/src/ontology/Makefile b/src/ontology/Makefile index c1359dc68..0fe361470 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for uberon # Generated using ontology-development-kit -# ODK Version: v1.5 +# ODK Version: v1.5.2 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= efb88af827f2af6cc513d695dc0dd59380e3e34c4ecf16d3648ebcfbba0aa64f +CONFIG_HASH= 9531f9cc87d9bbbcf0d424b5845e95234e9cd34df6d28bdbb856a4ba7b5557ad # ---------------------------------------- @@ -47,7 +47,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format SPARQL_EXPORTS = basic-report -ODK_VERSION_MAKEFILE = v1.5 +ODK_VERSION_MAKEFILE = v1.5.2 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -370,7 +370,7 @@ ALLSEED = $(PRESEED) $(TMPDIR)/all_pattern_terms.txt \ $(IMPORTSEED): $(ALLSEED) | $(TMPDIR) if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi -ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 +ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 OMO:0002000 # ---------------------------------------- # Import modules diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 2f3f76f9f..ffa2e7ff8 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 "2024-08-06") + +Annotation(owl:versionInfo "2024-08-13") Declaration(Class()) Declaration(Class()) @@ -12466,6 +12466,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12546,7 +12547,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12711,6 +12711,29 @@ AnnotationAssertion(rdfs:label "lat AnnotationAssertion( "tooth SubClassOf 'never in taxon' value 'Aves'") AnnotationAssertion( "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.") AnnotationAssertion( "Class: ?X DisjointWith: RO_0002162 some ?Y ") +AnnotationAssertion( "PREFIX rdfs: +PREFIX owl: +PREFIX in_taxon: +PREFIX never_in_taxon: +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?x owl:disjointWith [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . + ?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom [ + a owl:Class ; + owl:complementOf ?taxon + ] + ] . +} +WHERE { + ?x never_in_taxon: ?taxon . +}") AnnotationAssertion(rdfs:label "never in taxon") AnnotationAssertion(rdfs:seeAlso ) @@ -12718,6 +12741,25 @@ AnnotationAssertion(rdfs:seeAlso "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.") AnnotationAssertion( "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)") +AnnotationAssertion( "PREFIX owl: +PREFIX part_of: +PREFIX mutually_spatially_disjoint_with: +CONSTRUCT { + part_of: a owl:ObjectProperty . + [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?x ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?y + ] + ] +} +WHERE { + ?x mutually_spatially_disjoint_with: ?y . +}") AnnotationAssertion(rdfs:label "mutually spatially disjoint with"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) @@ -12738,6 +12780,30 @@ AnnotationAssertion(rdfs:seeAlso (present in taxon) AnnotationAssertion( "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S") +AnnotationAssertion( "PREFIX rdfs: +PREFIX owl: +PREFIX in_taxon: +PREFIX present_in_taxon: +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?witness rdfs:label ?label . + ?witness rdfs:subClassOf ?x . + ?witness rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . +} +WHERE { + ?x present_in_taxon: ?taxon . + BIND(IRI(CONCAT( + \"http://purl.obolibrary.org/obo/RO_0002175#\", + MD5(STR(?x)), + \"-\", + MD5(STR(?taxon)) + )) as ?witness) + BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label) +}") AnnotationAssertion(rdfs:comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.") AnnotationAssertion(rdfs:label "present in taxon"@en) AnnotationAssertion(rdfs:seeAlso ) @@ -46784,10 +46850,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "http://www.ncbi.nlm.nih.gov/books/NBK53245/") AnnotationAssertion(rdfs:label "placental villus capillary endothelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian fibroblast) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 731fb990b..98542aec1 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -110900,7 +110900,6 @@ xref: XAO:0000326 is_a: UBERON:0001048 {source="XAO"} ! primordium is_a: UBERON:0003104 ! mesenchyme relationship: develops_from UBERON:0004872 {source="XAO"} ! splanchnic layer of lateral plate mesoderm -relationship: part_of UBERON:0005602 {source="EHDAA2-modified"} ! dorsal mesogastrium property_value: external_ontology_notes "check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme" xsd:string {external_ontology="EMAPA"} [Term] @@ -143152,7 +143151,6 @@ is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: develops_from UBERON:0011095 ! vertebra pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002412 ! vertebra relationship: present_in_taxon NCBITaxon:7764 {notes="vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist", source="PMC3157150"} ! Eptatretus burgeri property_value: external_ontology_notes "This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups" xsd:string {external_ontology="EHDAA2"} @@ -143166,7 +143164,7 @@ xref: VHOG:0000582 intersection_of: UBERON:0010913 ! vertebral element intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation relationship: develops_from UBERON:0003089 {source="EHDAA2-abduced"} ! sclerotome -relationship: has_potential_to_develop_into UBERON:0002412 ! vertebra +relationship: has_potential_to_develop_into UBERON:0011094 ! vertebra cartilage element [Term] id: UBERON:0011096 diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml index 1e024d4d0..716ad0d48 100644 --- a/src/ontology/uberon-odk.yaml +++ b/src/ontology/uberon-odk.yaml @@ -29,6 +29,10 @@ release_artefacts: - custom-common-anatomy edit_format: obo import_group: + annotation_properties: + - rdfs:label + - IAO:0000115 + - OMO:0002000 use_base_merging: TRUE slme_individuals: exclude exclude_iri_patterns: