diff --git a/.gitignore b/.gitignore index 6326cb8..2ce18ab 100644 --- a/.gitignore +++ b/.gitignore @@ -66,4 +66,4 @@ src/patterns/data/**/*.txt src/patterns/pattern_owl_seed.txt src/patterns/all_pattern_terms.txt -# End of ODK-managed rules \ No newline at end of file +# End of ODK-managed rules diff --git a/src/ontology/Makefile b/src/ontology/Makefile index a46b907..464677e 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -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= 22b896ff37a2178cf683be4df092a84aca4cad6aac001f4a85792c7351452992 +CONFIG_HASH= bfc9223094875f6270fa84b7327623c74b217980c60850a5c0942756ce12dfe9 # ---------------------------------------- @@ -417,6 +417,25 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms.txt \ .PRECIOUS: $(IMPORTDIR)/%_import.owl +## Module for ontology: ms (slme) +$(IMPORTDIR)/ms_import.owl: $(MIRRORDIR)/ms.owl $(IMPORTDIR)/ms_terms.txt $(IMPORTSEED) | all_robot_plugins + $(ROBOT) annotate --input $< --remove-annotations \ + odk:normalize --add-source true \ + extract --term-file $(IMPORTDIR)/ms_terms.txt $(T_IMPORTSEED) \ + --copy-ontology-annotations true --force true \ + --individuals include \ + --method STAR \ + remove $(foreach p, $(ANNOTATION_PROPERTIES), --term $(p)) \ + --term rdfs:label \ + --term IAO:0000115 \ + --term OMO:0002000 \ + --term-file $(IMPORTDIR)/ms_terms.txt $(T_IMPORTSEED) \ + --select complement --select annotation-properties \ + odk:normalize --base-iri http://purl.obolibrary.org/obo \ + --subset-decls true --synonym-decls true \ + repair --merge-axiom-annotations true \ + $(ANNOTATE_CONVERT_FILE) + endif # IMP=true .PHONY: refresh-imports diff --git a/src/ontology/camo-edit.owl b/src/ontology/camo-edit.owl index 87716e7..ab95e1f 100644 --- a/src/ontology/camo-edit.owl +++ b/src/ontology/camo-edit.owl @@ -128,26 +128,31 @@ SubClassOf( (Survey) +AnnotationAssertion(dcterms:description "Data obtained from a survey or questionnaire given to a participant or their representative.") AnnotationAssertion(rdfs:label "Survey"@en) SubClassOf( ) # Class: (Research Assessment) +AnnotationAssertion(dcterms:description "Data obtained by research staff for the study.") AnnotationAssertion(rdfs:label "Research Assessment"@en) SubClassOf( ) # Class: (Interview) +AnnotationAssertion(dcterms:description "Data obtained directly by research staff examining the participant.") AnnotationAssertion(rdfs:label "Interview"@en) SubClassOf( ) # Class: (Physical Examination) +AnnotationAssertion(dcterms:description "Data obtained by research staff interviewing participants, representatives, or others.") AnnotationAssertion(rdfs:label "Physical Examination"@en) SubClassOf( ) # Class: (Electronic Health Record) +AnnotationAssertion(dcterms:description "Data obtained directly from an Electronic Health Record.") AnnotationAssertion(rdfs:label "Electronic Health Record"@en) SubClassOf( ) @@ -156,33 +161,39 @@ SubClassOf( "Asserter"@en) SubClassOf( ) -# Class: (Investigator Asserted) +# Class: (Research Staff Asserted) -AnnotationAssertion(rdfs:label "Investigator Asserted"@en) +AnnotationAssertion(dcterms:description "Assertion made by research staff.") +AnnotationAssertion(rdfs:label "Research Staff Asserted"@en) SubClassOf( ) # Class: (Healthcare Asserted) +AnnotationAssertion(dcterms:description "Assertion documented by a healthcare system or provider.") AnnotationAssertion(rdfs:label "Healthcare Asserted"@en) SubClassOf( ) # Class: (Participant or Representative Asserted) +AnnotationAssertion(dcterms:description "Assertion made by a study participant, their representative, or some combination.") AnnotationAssertion(rdfs:label "Participant or Representative Asserted"@en) SubClassOf( ) # Class: (Participant Asserted) +AnnotationAssertion(dcterms:description "Assertion made by a study participant.") AnnotationAssertion(rdfs:label "Participant Asserted"@en) SubClassOf( ) # Class: (Representative Asserted) +AnnotationAssertion(dcterms:description "Assertion made by a study participant's representative or representatives.") AnnotationAssertion(rdfs:label "Representative Asserted"@en) SubClassOf( ) # Class: (Caregiver Asserted) +AnnotationAssertion(dcterms:description "Assertion made by a study participant's caregiver or caregivers.") AnnotationAssertion(rdfs:label "Caregiver Asserted"@en) SubClassOf( ) @@ -221,6 +232,7 @@ SubClassOf( (Group) +AnnotationAssertion(dcterms:description "A group of entities or things being assessed as a whole.") AnnotationAssertion(rdfs:label "Group"@en) SubClassOf( ) diff --git a/src/ontology/camo-idranges.owl b/src/ontology/camo-idranges.owl index 59f8e5b..0582f8b 100644 --- a/src/ontology/camo-idranges.owl +++ b/src/ontology/camo-idranges.owl @@ -33,7 +33,7 @@ AnnotationProperty: allocatedto: Datatype: idrange:1 Annotations: - allocatedto: "ONTOLOGY-CREATOR" + allocatedto: "Robert Carroll" EquivalentTo: xsd:integer[>= 0 , <= 999999] diff --git a/src/ontology/camo-odk.yaml b/src/ontology/camo-odk.yaml index 0b36762..e69f35c 100644 --- a/src/ontology/camo-odk.yaml +++ b/src/ontology/camo-odk.yaml @@ -19,6 +19,8 @@ export_formats: import_group: products: - id: ms + module_type: slme + module_type_slme: STAR robot_java_args: '-Xmx8G' documentation: documentation_system: mkdocs \ No newline at end of file diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 285228b..a652a3c 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,6 +1,6 @@ - - + + - + \ No newline at end of file diff --git a/src/ontology/imports/ms_import.owl b/src/ontology/imports/ms_import.owl index 6e78478..e49fb95 100644 --- a/src/ontology/imports/ms_import.owl +++ b/src/ontology/imports/ms_import.owl @@ -7,34 +7,16 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2026-08-17") +Annotation(owl:versionInfo "2026-08-18") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -############################ -# Object Properties -############################ - -# Object Property: (part_of) - -AnnotationAssertion(rdfs:label "part_of") -TransitiveObjectProperty() - -# Object Property: (has value type) - -AnnotationAssertion( "'Entity A' has value type 'Entity B', such as xsd:float.") -AnnotationAssertion(rdfs:label "has value type") - - ############################ # Classes