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Merged
merged 1 commit into from
Aug 11, 2023
Merged

Add hra_depiction_3d_images component #3015

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1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -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 |
7 changes: 4 additions & 3 deletions src/ontology/Makefile
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@@ -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

Expand Down Expand Up @@ -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 [email protected] && mv [email protected] $@
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
Expand Down Expand Up @@ -395,6 +395,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)




# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
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1 change: 1 addition & 0 deletions src/ontology/catalog-dynamic.xml
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Expand Up @@ -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>
1,284 changes: 1,284 additions & 0 deletions src/ontology/components/hra_depiction_3d_images.owl
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3 changes: 2 additions & 1 deletion src/ontology/uberon-odk.yaml
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Expand Up @@ -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
7 changes: 7 additions & 0 deletions src/ontology/uberon.Makefile
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Expand Up @@ -1795,6 +1795,13 @@ $(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
# ----------------------------------------
Expand Down
3 changes: 2 additions & 1 deletion src/sparql/illegal-annotation-property-violation.sparql
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Expand Up @@ -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_"))
}