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Import OMO terms #3092

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merged 4 commits into from
Oct 26, 2023
Merged

Import OMO terms #3092

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2a10fb6
import OMO terms
anitacaron Oct 13, 2023
dbbce90
Merge branch 'master' into anitacaron/issue3058
anitacaron Oct 25, 2023
3240ea7
update import with OMO:0003011
anitacaron Oct 25, 2023
a58b5f7
Merge branch 'master' into anitacaron/issue3058
Oct 26, 2023
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1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -28,6 +28,7 @@ These are the current imports in UBERON
| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
| nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
| orcidio | https://w3id.org/orcidio/orcidio.owl | None |
| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |

## 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:
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17 changes: 16 additions & 1 deletion src/ontology/Makefile
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Expand Up @@ -114,7 +114,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio
IMPORTS = pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio omo

IMPORT_ROOTS = $(IMPORTDIR)/merged_import
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -339,6 +339,12 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined

.PRECIOUS: $(IMPORTDIR)/%_import.owl

## Module for ontology: omo

$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/omo_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi


.PHONY: refresh-imports
refresh-imports:
Expand Down Expand Up @@ -505,6 +511,15 @@ mirror-orcidio: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://w3id.org/orcidio/orcidio.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: omo
.PHONY: mirror-omo
.PRECIOUS: $(MIRRORDIR)/omo.owl
mirror-omo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi

ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
MERGE_MIRRORS = true

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