Merge pull request #247 from ApolloDev/update-go-import

Create go import

.github/workflows/qc.yml

@@ -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:

docs/odk-workflows/RepositoryFileStructure.md

@@ -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:

src/ontology/Makefile

@@ -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
 
@@ -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
 
 
 # ----------------------------------------
@@ -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')
@@ -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)
@@ -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:
@@ -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

src/ontology/apollo_sv-odk.yaml

@@ -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: |

src/ontology/catalog-v001.xml

@@ -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>

src/ontology/imports/geo_import.owl

@@ -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>))
@@ -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)