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Scott Christley
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add GAZ
1 parent ab0e163 commit fa6d7fb

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‎docs/odk-workflows/RepositoryFileStructure.md‎

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@@ -21,6 +21,7 @@ These are the current imports in AK-ONTOLOGY
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| CL | http://purl.obolibrary.org/obo/CL.owl | None |
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| DOID | http://purl.obolibrary.org/obo/DOID.owl | None |
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| EXO | http://purl.obolibrary.org/obo/EXO.owl | None |
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| GAZ | http://purl.obolibrary.org/obo/GAZ.owl | None |
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| IAO | http://purl.obolibrary.org/obo/IAO.owl | None |
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| OBI | http://purl.obolibrary.org/obo/OBI.owl | None |
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| OGMS | http://purl.obolibrary.org/obo/OGMS.owl | None |

‎src/ontology/Makefile‎

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# More information: https://github.com/INCATools/ontology-development-kit/
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# Fingerprint of the configuration file when this Makefile was last generated
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CONFIG_HASH= cdc9b63b8b8955e2b712546db4b77127d976453f51db8b288c6c5790c1404ac5
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CONFIG_HASH= 39068016a7a3bd9ee8180df6a20ff316731d4d5dca9057f0ff91b48fdd6cf9de
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# ----------------------------------------
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# ----------------------------------------
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IMPORTS = APOLLO_SV BFO CL DOID EXO IAO OBI OGMS OMRSE PATO RO SBO UBERON UO VO
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IMPORTS = APOLLO_SV BFO CL DOID EXO GAZ IAO OBI OGMS OMRSE PATO RO SBO UBERON UO VO
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IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
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IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -364,6 +364,13 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
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.PRECIOUS: $(IMPORTDIR)/%_import.owl
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## Module for ontology: GAZ
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$(IMPORTDIR)/GAZ_import.owl: $(MIRRORDIR)/GAZ.owl $(IMPORTDIR)/GAZ_terms_combined.txt
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if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/GAZ_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
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query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
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$(ANNOTATE_CONVERT_FILE); fi
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.PHONY: refresh-imports
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refresh-imports:
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$(ROBOT) convert -i $(TMPDIR)/EXO-download.owl -o $(TMPDIR)/$@.owl
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## ONTOLOGY: GAZ
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.PHONY: mirror-GAZ
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.PRECIOUS: $(MIRRORDIR)/GAZ.owl
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ifeq ($(strip $(IMP_LARGE)),true)
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mirror-GAZ: | $(TMPDIR)
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curl -L $(OBOBASE)/GAZ.owl --create-dirs -o $(TMPDIR)/GAZ-download.owl --retry 4 --max-time 200 && \
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$(ROBOT) convert -i $(TMPDIR)/GAZ-download.owl -o $(TMPDIR)/$@.owl
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else
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mirror-GAZ:
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@echo "Not refreshing GAZ because refreshing large imports is disabled (IMP_LARGE=$(IMP_LARGE))."
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endif
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## ONTOLOGY: IAO
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.PHONY: mirror-IAO
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.PRECIOUS: $(MIRRORDIR)/IAO.owl

‎src/ontology/ak-ontology-odk.yaml‎

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@@ -9,8 +9,8 @@ import_group:
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- id: CL
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- id: DOID
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- id: EXO
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# - id: GAZ
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# is_large: TRUE
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- id: GAZ
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is_large: TRUE
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- id: IAO
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# - id: NCBITaxon
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# is_large: TRUE

‎src/ontology/imports/APOLLO_SV_import.owl‎

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‎src/ontology/imports/BFO_import.owl‎

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Ontology(<http://purl.obolibrary.org/obo/ak-ontology/imports/BFO_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2024-04-26/imports/BFO_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2025-07-29/imports/BFO_import.owl>
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Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
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Annotation(owl:versionInfo "2024-04-26")
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Annotation(owl:versionInfo "2025-07-29")
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))

‎src/ontology/imports/CL_import.owl‎

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‎src/ontology/imports/DOID_import.owl‎

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Ontology(<http://purl.obolibrary.org/obo/ak-ontology/imports/DOID_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2024-04-26/imports/DOID_import.owl>
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Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/doid/releases/2024-03-28/doid.owl>)
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Annotation(owl:versionInfo "2024-04-26")
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2025-07-29/imports/DOID_import.owl>
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Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/doid/releases/2025-06-27/doid.owl>)
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Annotation(owl:versionInfo "2025-07-29")
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000700>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/language>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))

‎src/ontology/imports/EXO_import.owl‎

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Ontology(<http://purl.obolibrary.org/obo/ak-ontology/imports/EXO_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2024-04-26/imports/EXO_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2025-07-29/imports/EXO_import.owl>
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Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/exo/releases/2022-06-29/exo.owl>)
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Annotation(owl:versionInfo "2024-04-26")
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Annotation(owl:versionInfo "2025-07-29")
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))

‎src/ontology/imports/GAZ_terms.txt‎

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‎src/ontology/imports/IAO_import.owl‎

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Ontology(<http://purl.obolibrary.org/obo/ak-ontology/imports/IAO_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2024-04-26/imports/IAO_import.owl>
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<http://purl.obolibrary.org/obo/ak-ontology/releases/2025-07-29/imports/IAO_import.owl>
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Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
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Annotation(owl:versionInfo "2024-04-26")
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Annotation(owl:versionInfo "2025-07-29")
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

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