Merge pull request #3015 from obophenotype/component-3d-images

Add hra_depiction_3d_images component
obophenotype · Aug 11, 2023 · 3074ac3 · 3074ac3
2 parents 91bb8d3 + cfa0914
commit 3074ac3
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Showing 7 changed files with 1,301 additions and 5 deletions.
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -43,3 +43,4 @@ These are the components in UBERON
 | in-subset.owl | None |
 | hra_subset.owl | None |
 | vasculature_class.owl | None |
+| hra_depiction_3d_images.owl | None |
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.1
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -44,14 +44,14 @@ 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 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.4.1
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -395,6 +395,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

diff --git a/src/ontology/catalog-dynamic.xml b/src/ontology/catalog-dynamic.xml
@@ -146,5 +146,6 @@
     <uri name="http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl" uri="components/vasculature_class.owl"/>
     <uri name="http://purl.obolibrary.org/obo/uberon/components/in-subset.owl" uri="components/in-subset.owl"/>
     <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl" uri="components/hra_subset.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl" uri="components/hra_depiction_3d_images.owl"/>
 
 </catalog>
diff --git a/src/ontology/components/hra_depiction_3d_images.owl b/src/ontology/components/hra_depiction_3d_images.owl
diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
@@ -120,4 +120,5 @@ components:
     - filename: mappings.owl
     - filename: in-subset.owl
     - filename: hra_subset.owl
-    - filename: vasculature_class.owl
+    - filename: vasculature_class.owl
+    - filename: hra_depiction_3d_images.owl
diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
@@ -1793,6 +1793,13 @@ $(TMPDIR)/hra_subset.owl:
 $(COMPONENTSDIR)/hra_subset.owl: $(TMPDIR)/hra_subset.owl
 	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
 
+3D_IMAGES_COMP_URL="https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/hra_uberon_3d_images.owl"
+$(TMPDIR)/hra_depiction_3d_images.owl:
+	wget $(3D_IMAGES_COMP_URL) -O $@
+
+$(COMPONENTSDIR)/hra_depiction_3d_images.owl: $(TMPDIR)/hra_depiction_3d_images.owl
+	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
+
 # ----------------------------------------
 # DEAD SIMPLE DESIGN PATTERNS
 # ----------------------------------------

diff --git a/src/sparql/illegal-annotation-property-violation.sparql b/src/sparql/illegal-annotation-property-violation.sparql
@@ -75,7 +75,8 @@ SELECT DISTINCT ?annotation WHERE {
     <http://www.w3.org/2000/01/rdf-schema#seeAlso>,
     <http://www.w3.org/2004/02/skos/core#closeMatch>,
     <http://www.w3.org/2002/07/owl#deprecated>,
-    <http://xmlns.com/foaf/0.1/depicted_by>
+    <http://xmlns.com/foaf/0.1/depicted_by>,
+    <http://xmlns.com/foaf/0.1/depiction>
   ))
   FILTER (isIRI(?subj) && STRSTARTS(str(?subj), "http://purl.obolibrary.org/obo/UBERON_"))
 }