Add FOODON:device specification

NFDI4Chem · Jan 9, 2024 · 0cdcc91 · 0cdcc91
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commit 0cdcc91
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -26,6 +26,7 @@ These are the current imports in VIBSO
 | stato | http://purl.obolibrary.org/obo/stato.owl | None |
 | uo | http://purl.obolibrary.org/obo/uo.owl | custom |
 | chebi | http://purl.obolibrary.org/obo/chebi.owl | None |
+| foodon | http://purl.obolibrary.org/obo/foodon.owl | None |
 
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -108,7 +108,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  bfo ro omo iao chmo pato obi stato uo chebi
+IMPORTS =  bfo ro omo iao chmo pato obi stato uo chebi foodon
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -517,6 +517,16 @@ mirror-chebi: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
+## ONTOLOGY: foodon
+.PHONY: mirror-foodon
+.PRECIOUS: $(MIRRORDIR)/foodon.owl
+mirror-foodon: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/foodon.owl --create-dirs -o $(MIRRORDIR)/foodon.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/foodon.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/FOODON --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -23,5 +23,7 @@
         <uri name="http://purl.obolibrary.org/obo/vibso/imports/chebi_import.obo" uri="imports/chebi_import.obo"/>
         <uri name="http://purl.obolibrary.org/obo/vibso/imports/uo_import.owl" uri="imports/uo_import.owl"/>
         <uri name="http://purl.obolibrary.org/obo/vibso/imports/uo_import.obo" uri="imports/uo_import.obo"/>
+        <uri name="http://purl.obolibrary.org/obo/vibso/imports/foodon_import.owl" uri="imports/foodon_import.owl"/>
+        <uri name="http://purl.obolibrary.org/obo/vibso/imports/foodon_import.obo" uri="imports/foodon_import.obo"/>
     </group>
 </catalog>
diff --git a/src/ontology/imports/foodon_import.owl b/src/ontology/imports/foodon_import.owl
@@ -0,0 +1,59 @@
+Prefix(:=<http://purl.obolibrary.org/obo/vibso/imports/foodon_import.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/vibso/imports/foodon_import.owl>
+<http://purl.obolibrary.org/obo/vibso/releases/2024-01-09/imports/foodon_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/foodon/releases/2023-05-03/foodon.owl>)
+Annotation(owl:versionInfo "2024-01-09")
+
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
+Declaration(Class(<http://purl.obolibrary.org/obo/FOODON_00004086>))
+Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))
+Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000032>))
+Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000033>))
+Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9606>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000245>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IAO_0000136>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000293>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000299>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000087>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000112>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000114>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000118>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000231>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/date>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/description>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#default-namespace>))
+Declaration(Datatype(xsd:date))
+
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/FOODON_00004086> (device specification)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/FOODON_00004086> <http://purl.obolibrary.org/obo/IAO_0000428>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FOODON_00004086> "A directive information entity which specifies a device and its settings for use within a plan specification."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/FOODON_00004086> <http://orcid.org/0000-0002-8844-9165>)
+AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/FOODON_00004086> "2021-11-29T21:53:39Z"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FOODON_00004086> "device specification"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/FOODON_00004086> <http://purl.obolibrary.org/obo/IAO_0000033>)
+
+
+)
diff --git a/src/ontology/imports/foodon_terms.txt b/src/ontology/imports/foodon_terms.txt
@@ -0,0 +1 @@
+FOODON:00004086 # device specification
diff --git a/src/ontology/vibso-edit.owl b/src/ontology/vibso-edit.owl
@@ -30,6 +30,7 @@ Import(<http://purl.obolibrary.org/obo/vibso/imports/pato_import.owl>)
 Import(<http://purl.obolibrary.org/obo/vibso/imports/ro_import.owl>)
 Import(<http://purl.obolibrary.org/obo/vibso/imports/stato_import.owl>)
 Import(<http://purl.obolibrary.org/obo/vibso/imports/uo_import.owl>)
+Import(<http://purl.obolibrary.org/obo/vibso/imports/foodon_import.owl>)
 Annotation(dcterms:contributor <https://orcid.org/0000-0002-1595-3213>)
 Annotation(dcterms:contributor <https://orcid.org/0000-0002-2239-3955>)
 Annotation(dcterms:contributor <https://orcid.org/0000-0002-4378-6061>)

diff --git a/src/ontology/vibso-odk.yaml b/src/ontology/vibso-odk.yaml
@@ -62,6 +62,8 @@ import_group:
     is_large: true
     use_gzipped: true
     make_base: true
+  - id: foodon
+    make_base: true
 components:
   products:
     - filename: vibso_classes.owl  # TSV templates to define VIBSO classes