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Create go import #247

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merged 3 commits into from
Aug 15, 2024
Merged

Create go import #247

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3e6ef68
added GO import, defined new class 'reproduction' as the disjunction …
hoganwr Aug 12, 2024
325373e
updated RO import vis make all_imports, so they all got updated. Incl…
hoganwr Aug 13, 2024
81fec41
adding some stuff generated by update_repo, which I had to run to add…
hoganwr Aug 13, 2024
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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:v1.5
container: obolibrary/odkfull:v1.5.2

# 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 @@ -21,6 +21,7 @@ These are the current imports in APOLLO_SV
| geo | http://purl.obolibrary.org/obo/geo/dev/geo.owl | mirror |
| ido | http://purl.obolibrary.org/obo/ido.owl | slme |
| mf | http://purl.obolibrary.org/obo/mf.owl | slme |
| go | http://purl.obolibrary.org/obo/go.owl | slme |

## 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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24 changes: 20 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: v1.5
# ODK Version: v1.5.2
# ----------------------------------------
# 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= 8c83508f90aec6eebe48cba22814c2547bdf197ecf902ac8f55664f6ae708683
CONFIG_HASH= c731446a515442f3b378e0f8803a2a533d775453ddcf1c23a26ddaed7564e0a1


# ----------------------------------------
Expand Down Expand Up @@ -52,7 +52,7 @@ REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range
SPARQL_EXPORTS = basic-report
ODK_VERSION_MAKEFILE = v1.5
ODK_VERSION_MAKEFILE = v1.5.2

TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
Expand Down Expand Up @@ -165,7 +165,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = ro pno geo ido mf
IMPORTS = ro pno geo ido mf go

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -423,6 +423,14 @@ $(IMPORTDIR)/mf_import.owl: $(MIRRORDIR)/mf.owl $(IMPORTDIR)/mf_terms_combined.t
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: go

$(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/go_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \
query --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 @@ -493,6 +501,14 @@ mirror-mf: | $(TMPDIR)
$(ROBOT) convert -i $(TMPDIR)/mf-download.owl -o $(TMPDIR)/$@.owl


## ONTOLOGY: go
.PHONY: mirror-go
.PRECIOUS: $(MIRRORDIR)/go.owl
mirror-go: | $(TMPDIR)
curl -L $(OBOBASE)/go.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/go-download.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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970 changes: 35 additions & 935 deletions src/ontology/apollo_sv-edit.owl
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3 changes: 3 additions & 0 deletions src/ontology/apollo_sv-odk.yaml
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Expand Up @@ -36,6 +36,9 @@ import_group:
- id: mf
module_type: slme
slme_individuals: exclude
- id: go
module_type: slme
slme_individuals: exclude
use_custom_import_module: TRUE
robot_java_args: '-Xmx8G'
custom_makefile_header: |
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2 changes: 2 additions & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -18,6 +18,8 @@
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/mf_import.owl" uri="imports/mf_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/mf_import.obo" uri="imports/mf_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/apollo_sv/imports/go_import.obo" uri="imports/go_import.obo"/>

</group>
</catalog>
6 changes: 3 additions & 3 deletions src/ontology/imports/geo_import.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/apollo_sv/imports/geo_import.owl>
<http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/imports/geo_import.owl>
Annotation(owl:versionInfo "2024-04-19")
<http://purl.obolibrary.org/obo/apollo_sv/releases/2024-08-13/imports/geo_import.owl>
Annotation(owl:versionInfo "2024-08-13")

Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000008>))
Declaration(Class(<http://purl.obolibrary.org/obo/APOLLO_SV_00000032>))
Expand Down Expand Up @@ -2690,7 +2690,7 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GEO_000000006>
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GEO_000000006> "geopolitical dependency"@en)
SubClassOf(<http://purl.obolibrary.org/obo/GEO_000000006> <http://purl.obolibrary.org/obo/GEO_000000004>)

# Class: <http://purl.obolibrary.org/obo/GEO_000000007> (aggregate of major administrative subdivisions)
# Class: <http://purl.obolibrary.org/obo/GEO_000000007> (group of major administrative subdivisions)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GEO_000000007> "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/GEO_000000007> "Amanda Hicks"@en)
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