Merge pull request #17 from h3abionet/split-synonyms

Use oboInOwl:hasExactSynonyms
h3abionet · Dec 20, 2023 · 9c5581b · 9c5581b
2 parents da71fa9 + 809b8c0
commit 9c5581b
Show file tree

Hide file tree

Showing 7 changed files with 406 additions and 21 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,44 @@
-src/ontology/tmp/
-src/ontology/afpo.json
-src/ontology/afpo.obo
+.DS_Store
+semantic.cache
+bin/
+
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+
+.github/token.txt
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
 src/ontology/afpo.owl
+src/ontology/afpo.obo
+src/ontology/afpo.json
+src/ontology/afpo-base.*
+src/ontology/afpo-basic.*
+src/ontology/afpo-full.*
+src/ontology/afpo-simple.*
+src/ontology/afpo-simple-non-classified.*
+
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-afpo-edit.owl
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+src/ontology/imports/*_terms_combined.txt
+
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for afpo
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use afpo.Makefile instead
 
@@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.4.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -109,7 +109,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS = 
+IMPORTS =  omo
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -293,7 +293,7 @@ ALLSEED = $(PRESEED) \
 $(IMPORTSEED): $(ALLSEED) | $(TMPDIR)
 	if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi
 
-ANNOTATION_PROPERTIES=
+ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 
 
 # ----------------------------------------
 # Import modules
@@ -309,6 +309,12 @@ $(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
 
 
 
+$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
+		extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
+		$(ANNOTATE_CONVERT_FILE); fi
+
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
 
 
@@ -342,6 +348,15 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 
 
 
+## 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 $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -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

diff --git a/src/ontology/afpo-edit.ofn b/src/ontology/afpo-edit.ofn
@@ -9,6 +9,7 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/afpo.owl>
+Import(<http://purl.obolibrary.org/obo/afpo/imports/omo_import.owl>)
 Annotation(dcterms:contributor <https://orcid.org/0000-0001-5868-4204>)
 Annotation(dcterms:contributor <https://orcid.org/0000-0001-8351-264X>)
 Annotation(dcterms:contributor <https://orcid.org/0000-0001-8801-5781>)
@@ -492,7 +493,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/AfPO_0000580>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/AfPO_0000441>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/AfPO_0000447>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/AfPO_0000089>))
-Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/AfPO_0000143>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/AfPO_0000152>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/AfPO_0000221>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/AfPO_0000222>))
@@ -534,6 +534,7 @@ Declaration(AnnotationProperty(dcterms:title))
 Declaration(AnnotationProperty(<http://webprotege.stanford.edu/project/AfPO#language:crossref>))
 Declaration(AnnotationProperty(<http://webprotege.stanford.edu/project/AfPO#population:crossref>))
 Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#creation_date>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
 Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#altLabel>))
 ############################
 #   Annotation Properties
@@ -546,10 +547,6 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date>
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AfPO_0000089> "language:glottolog:wgs84")
 SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/AfPO_0000089> <http://webprotege.stanford.edu/project/AfPO#language:crossref>)
 
-# Annotation Property: <http://purl.obolibrary.org/obo/AfPO_0000143> (synonym)
-
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AfPO_0000143> "synonym")
-
 # Annotation Property: <http://purl.obolibrary.org/obo/AfPO_0000152> (population:genetic:study)
 
 AnnotationAssertion(dcterms:contributor <http://purl.obolibrary.org/obo/AfPO_0000152> <https://orcid.org/0000-0001-9988-3250>)
@@ -3183,7 +3180,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000128> ObjectSomeValuesFrom(<h
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000089> <http://purl.obolibrary.org/obo/AfPO_0000131> "Mossi
 11°57'N, 1°19'W
 11.95, -1.32")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000143> <http://purl.obolibrary.org/obo/AfPO_0000131> "Mooré, Mòoré, Mõõré, Moré, Moshi, Moore, More")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000152> <http://purl.obolibrary.org/obo/AfPO_0000131> <https://www.ncbi.nlm.nih.gov/pubmed/26614524>)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000221> <http://purl.obolibrary.org/obo/AfPO_0000131> <http://www-01.sil.org/iso639-3/documentation.asp?id=mos>)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000223> <http://purl.obolibrary.org/obo/AfPO_0000131> <http://glottolog.org/resource/languoid/id/moss1236.bigmap.html>)
@@ -3217,6 +3213,13 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000459> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000565> <http://purl.obolibrary.org/obo/AfPO_0000131> "Niger-Congo|Atlantic-Congo|Volta-Congo|North|Gur|Central|Northern|Oti-Volta|Western")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000566> <http://purl.obolibrary.org/obo/AfPO_0000131> "moss1236")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000567> <http://purl.obolibrary.org/obo/AfPO_0000131> "mos")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "Moore")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "Mooré")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "More")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "Moré")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "Moshi")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "Mòoré")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000131> "Mõõré")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AfPO_0000131> "Mossi")
 SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000131> <http://purl.obolibrary.org/obo/AfPO_0000151>)
 SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000131> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/AfPO_0000441> <http://purl.obolibrary.org/obo/AfPO_0000310>))
@@ -6372,7 +6375,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000089> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000089> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tedaga
 18°03'N, 14°46'E
 18.04, 14.77")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000143> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tabu, Tebu, Tebou, Tibu, Tibbu, Toda, Todga, Todaga, Tubu, Tuda, Tudaga, and Umbararo")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000152> <http://purl.obolibrary.org/obo/AfPO_0000307> <https://www.ncbi.nlm.nih.gov/pubmed/27889059>)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000223> <http://purl.obolibrary.org/obo/AfPO_0000307> <http://glottolog.org/resource/languoid/id/tebu1238.bigmap.html>)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000230> <http://purl.obolibrary.org/obo/AfPO_0000307> <http://glottolog.org/resource/languoid/id/tebu1238>)
@@ -6385,6 +6387,18 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000458> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000459> <http://purl.obolibrary.org/obo/AfPO_0000307> "2.25 millions")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000565> <http://purl.obolibrary.org/obo/AfPO_0000307> "Nilo-Saharan|Saharan")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000568> <http://purl.obolibrary.org/obo/AfPO_0000307> <https://www.101lasttribes.com/tribes/toubou.html>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tabu")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tebou")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tebu")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tibbu")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tibu")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Toda")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Todaga")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Todga")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tubu")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tuda")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Tudaga")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000307> "Umbararo")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AfPO_0000307> "Toubou")
 SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000307> <http://purl.obolibrary.org/obo/AfPO_0000265>)
 SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000307> <http://purl.obolibrary.org/obo/AfPO_0000270>)
@@ -9431,7 +9445,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000089> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000089> <http://purl.obolibrary.org/obo/AfPO_0000419> "Etebi
 4°47'N, 7°58'E
 4.79, 7.97")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000143> <http://purl.obolibrary.org/obo/AfPO_0000419> "Ekid")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000221> <http://purl.obolibrary.org/obo/AfPO_0000419> <http://www-01.sil.org/iso639-3/documentation.asp?id=eke>)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000223> <http://purl.obolibrary.org/obo/AfPO_0000419> <http://glottolog.org/resource/languoid/id/ekit1245.bigmap.html>)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000230> <http://purl.obolibrary.org/obo/AfPO_0000419> <http://glottolog.org/resource/languoid/id/ekit1245>)
@@ -9443,6 +9456,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000458> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000459> <http://purl.obolibrary.org/obo/AfPO_0000419> "0.3 millions")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000459> <http://purl.obolibrary.org/obo/AfPO_0000419> "Niger–Congo, Cross River")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/AfPO_0000567> <http://purl.obolibrary.org/obo/AfPO_0000419> "eke")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/AfPO_0000419> "Ekid")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AfPO_0000419> "Eket")
 SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000419> <http://purl.obolibrary.org/obo/AfPO_0000277>)
 SubClassOf(<http://purl.obolibrary.org/obo/AfPO_0000419> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/AfPO_0000441> <http://purl.obolibrary.org/obo/AfPO_0000033>))

diff --git a/src/ontology/afpo-odk.yaml b/src/ontology/afpo-odk.yaml
@@ -15,6 +15,9 @@ export_formats:
   - owl
   - obo
   - json
+import_group:
+  products:
+    - id: omo
 robot_java_args: "-Xmx8G"
 robot_report:
   use_labels: TRUE

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -1,11 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
 <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
-
-
-
-
-
-
+    <uri name="http://purl.obolibrary.org/obo/afpo/imports/omo_import.owl" uri="imports/omo_import.owl"/>
 </group>
 </catalog>