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Merged
hoganwr merged 3 commits into from
Mar 14, 2026
Merged

added BCIO import, included it's human behavior class, and reorganize… #269

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395b88d
added BCIO import, included it's human behavior class, and reorganize…
hoganwr Mar 13, 2026
46eb3bf
trying to make sure the GitHub checks can make mirror/bcio.owl
hoganwr Mar 13, 2026
fdf4844
added ifeq IMP, true so it doesn't run the BCIO import unless requested
hoganwr Mar 13, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/qc.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.6
container: obolibrary/odkfull:v1.6.1

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
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1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -26,6 +26,7 @@ These are the current imports in APOLLO_SV
| dron | http://purl.obolibrary.org/obo/dron.owl | filter |
| ogms | http://purl.obolibrary.org/obo/ogms.owl | filter |
| uberon | http://purl.obolibrary.org/obo/uberon.owl | filter |
| bcio | http://humanbehaviourchange.org/ontology/bcio.owl | custom |
## 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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21 changes: 17 additions & 4 deletions src/ontology/Makefile
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@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for apollo_sv
# 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 apollo_sv.Makefile instead

Expand All @@ -16,7 +16,7 @@
# 3. [Update repo to latest ODK](update_repo)

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= 0625a31aff99dcab0d48bca6e3dddd2614c7f65055668a9ae139332d9e4f5f5f
CONFIG_HASH= 6ee100eeff7bea98a4fcb53394f21f836ae9386cecca6a38ef47b0c9c6a71fd0


# ----------------------------------------
Expand Down Expand Up @@ -54,7 +54,7 @@ REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS = --clean-obo "strict drop-untranslatable-axioms"
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range
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

Expand Down Expand Up @@ -193,7 +193,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = ro geo ido mf go iao omrse dron ogms uberon
IMPORTS = ro geo ido mf go iao omrse dron ogms uberon bcio

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -543,6 +543,12 @@ $(IMPORTDIR)/omrse_import.owl: $(MIRRORDIR)/omrse.owl $(IMPORTDIR)/omrse_terms.t
repair --merge-axiom-annotations true \
$(ANNOTATE_CONVERT_FILE)

## Module for ontology: bcio (custom)
$(IMPORTDIR)/bcio_import.owl: $(MIRRORDIR)/bcio.owl
@echo "ERROR: You have configured bcio as a custom module;"
@echo " This rule needs to be overwritten in apollo_sv.Makefile!"
@false

endif # IMP=true

.PHONY: refresh-imports
Expand Down Expand Up @@ -655,6 +661,13 @@ mirror-uberon: | $(TMPDIR)
$(ROBOT) remove -i $(TMPDIR)/uberon-download.owl --base-iri http://purl.obolibrary.org/obo/UBERON_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl


## ONTOLOGY: bcio
.PHONY: mirror-bcio
.PRECIOUS: $(MIRRORDIR)/bcio.owl
mirror-bcio: | $(TMPDIR)
$(ROBOT) convert -I http://humanbehaviourchange.org/ontology/bcio.owl -o $(TMPDIR)/$@.owl


$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
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