Merge pull request #3679 from obophenotype/add-hra-skeleton-component

Add HRA skeleton component with 386 new skeletal terms

Author: RiveraAndrea83

docs/odk-workflows/RepositoryFileStructure.md

@@ -48,3 +48,4 @@ These are the components in UBERON
 | hra_subset.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/UB_ASCTB_subset.owl |
 | vasculature_class.owl | None |
 | hra_depiction_3d_images.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/hra_uberon_3d_images.owl |
+| hra_skeleton.owl | None |

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.6
+# ODK Version: v1.6.1
 # ----------------------------------------
 # 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=                0c09c67446229bbfacf685a28a496609521da5454d237d04715fcc7f737f6dee
+CONFIG_HASH=                4a0a1ec54c99987a5f925c045d14b90a8cea94072e234dab7b5b4841b16aa062
 
 
 # ----------------------------------------
@@ -50,7 +50,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        --clean-obo "strict drop-untranslatable-axioms"
 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 =      v1.6
+ODK_VERSION_MAKEFILE =      v1.6.1
 RELAX_OPTIONS =             --include-subclass-of true
 REDUCE_OPTIONS =            --include-subproperties true
 
@@ -59,7 +59,7 @@ 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)/disjoint_union_over.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/disjoint_union_over.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl $(COMPONENTSDIR)/hra_skeleton.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
@@ -492,6 +492,7 @@ recreate-components:
 		--assume-new=$(TMPDIR)/stamp-component-hra_subset.owl \
 		--assume-new=$(TMPDIR)/stamp-component-vasculature_class.owl \
 		--assume-new=$(TMPDIR)/stamp-component-hra_depiction_3d_images.owl \
+		--assume-new=$(TMPDIR)/stamp-component-hra_skeleton.owl \
 		COMP=true IMP=false MIR=true PAT=true all_components
 
 .PHONY: no-mirror-recreate-components
@@ -502,6 +503,7 @@ no-mirror-recreate-components:
 		--assume-new=$(TMPDIR)/stamp-component-hra_subset.owl \
 		--assume-new=$(TMPDIR)/stamp-component-vasculature_class.owl \
 		--assume-new=$(TMPDIR)/stamp-component-hra_depiction_3d_images.owl \
+		--assume-new=$(TMPDIR)/stamp-component-hra_skeleton.owl \
 		COMP=true IMP=false MIR=false PAT=true all_components
 
 .PHONY: recreate-%
@@ -566,6 +568,12 @@ $(COMPONENTSDIR)/hra_depiction_3d_images.owl: component-download-hra_depiction_3
 .PRECIOUS: $(COMPONENTSDIR)/hra_depiction_3d_images.owl
 endif # MIR=true
 
+$(COMPONENTSDIR)/hra_skeleton.owl: $(TEMPLATEDIR)/hra-skeleton.template.tsv $(TMPDIR)/stamp-component-hra_skeleton.owl
+	$(ROBOT) template  \
+		 --template $(TEMPLATEDIR)/hra-skeleton.template.tsv \
+		 $(ANNOTATE_CONVERT_FILE)
+.PRECIOUS: $(COMPONENTSDIR)/hra_skeleton.owl
+
 endif # COMP=true
 # ----------------------------------------
 # Mirroring upstream ontologies

src/ontology/catalog-v001.xml

@@ -9,6 +9,7 @@
     <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/vasculature_class.owl" uri="components/vasculature_class.owl" />
     <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl" uri="components/hra_depiction_3d_images.owl" />
+    <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_skeleton.owl" uri="components/hra_skeleton.owl" />
     <uri name="http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl" uri="../patterns/definitions.owl" />
   </group>
   <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public">