OBA-EFO alignment pipeline (not ready)

src/ontology/Makefile

@@ -410,3 +410,11 @@ components/gwas_template.owl: $(SRC) iri_dependencies/gwas_terms.tsv
 components/gwas_import.owl: components/gwas_template.owl
 	$(ROBOT) annotate -i $< -O "http://www.ebi.ac.uk/efo/components/gwas_import.owl" -o $@
 	rm components/gwas_template.owl
+
+# ----------------------------------------
+# OBA alignment Measurment Branch
+# -----------------------------------------
+
+align_oba:
+	make -f measurement.Makefile download_all
+	make -f measurement.Makefile reclassify.owl tmp/lost.owl

src/ontology/measurement.Makefile

@@ -0,0 +1,111 @@
+##################################
+### Cancer Mapping Pipeline ######
+##################################
+ROBOT=robot --catalog catalog-v001.xml
+#MAPPING_EFO_OBA=https://raw.githubusercontent.com/EBISPOT/efo/master/src/ontology/components/oba_efo_mappings.tsv
+MAPPING_OBA_EFO=https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-efo.sssom.tsv
+#MAPPING_AUGMENTED_EFO_OBA=https://docs.google.com/spreadsheets/d/e/2PACX-1vQb6EtOFekjNUAfnnQLfm6KDFY3DH8WPV2Gjb_2WXLofZ87HvmR2m0wchNxplpDGwzucsWy6BGfaILp/pub?gid=2147444170&single=true&output=tsv
+UNMAPPED_TERMS=https://docs.google.com/spreadsheets/d/e/2PACX-1vQb6EtOFekjNUAfnnQLfm6KDFY3DH8WPV2Gjb_2WXLofZ87HvmR2m0wchNxplpDGwzucsWy6BGfaILp/pub?gid=665705711&single=true&output=tsv
+OBA=http://purl.obolibrary.org/obo/oba.owl
+
+O1=efo-edit-tmp.owl
+O2=tmp/oba.owl
+MAP=tmp/oba_efo.tsv
+
+UNMAPPED_TERMS_FILTERED=tmp/keep_unmapped.owl
+TERMLIST=tmp/measurement_branch.tsv
+UNMAPPED=tmp/unmapped.tsv
+SPARQL_TERMLIST=sparql/efo_measurement.sparql
+SPARQL_LABELS=sparql/efo-original-labels.ru
+MIR=false
+
+tmp/ metadata/:
+	mkdir -p $@
+
+#tmp/efo_oba.tsv: | tmp/
+#	if [ $(MIR) = true ]; then wget "$(MAPPING_AUGMENTED_EFO_OBA)" -O [email protected] &&\
+#	cut -f 1,2 [email protected] > $@ && rm [email protected]; fi
+
+#	sed -i '1s/^/o1\to2\n/' [email protected]
+
+tmp/oba_efo.tsv: | tmp/
+	if [ $(MIR) = true ]; then wget "$(MAPPING_OBA_EFO)" -O $@; fi
+
+tmp/unmapped.tsv: | tmp/
+	if [ $(MIR) = true ]; then echo "EFO:0001444" > $@; fi
+
+$(O1):
+	cp efo-edit.owl $@
+
+MON=false
+tmp/oba.owl:
+	if [ $(MON) = true ]; then wget $(OBA) -O $@; fi
+
+download_all: tmp/oba_efo.tsv $(O1) tmp/oba.owl
+
+metadata/%_synonyms.tsv: | metadata/
+	$(ROBOT) query -i tmp/$*.owl --query sparql/synonyms.sparql $@
+
+metadata/%_labels.tsv: | metadata/
+	$(ROBOT) query -i tmp/$*.owl --query sparql/labels.sparql $@
+
+extract_metadata: metadata/oba_synonyms.tsv metadata/efo_synonyms.tsv
+extract_metadata: metadata/oba_labels.tsv metadata/efo_labels.tsv
+
+$(TERMLIST): $(O1) $(SPARQL_TERMLIST)
+	$(ROBOT) query -i $(O1) --query $(SPARQL_TERMLIST) $@
+	sed -i 's/[<>]//g' $@
+
+tmp/original_labels.ttl: $(O1) $(SPARQL_LABELS)
+	$(ROBOT) query -i $(O1) --query $(SPARQL_LABELS) $@
+
+# filter trim true will omit axioms in the measurement branch that mention entities
+# outside the measurement branch, in particular A sub R some C (where R, or C, are not in the measurement branch)
+tmp/reclassified.owl: $(O2) $(MAP) $(TERMLIST)
+	$(ROBOT) merge -i $(O2) \
+		query --update sparql/oba-labels-to-synonym.ru \
+		rename --mappings $(MAP) --allow-missing-entities true \
+		filter -T $(TERMLIST) --select "self annotations" -o $@
+
+$(UNMAPPED_TERMS_FILTERED): $(O1) $(UNMAPPED)
+	$(ROBOT) filter -i $< -T $(UNMAPPED) --trim false -o $@
+
+reclassify.owl: $(O1) tmp/reclassified.owl tmp/original_labels.ttl $(UNMAPPED_TERMS_FILTERED) $(TERMLIST)
+	$(ROBOT) remove -i $(O1) -T $(TERMLIST) \
+		merge -i tmp/reclassified.owl -i $(UNMAPPED_TERMS_FILTERED) -i tmp/original_labels.ttl -i tmp/lost_illegal.owl --collapse-import-closure false -o $@
+
+tmp/diff.txt: $(O1) reclassify.owl
+	$(ROBOT) diff --left $(O1) --right reclassify.owl -o $@
+
+tmp/diff2.txt: o1_merged.owl reclassify_merged.owl
+	$(ROBOT) diff --left o1_merged.owl --right reclassify_merged.owl -o $@
+
+
+# I want to get everything that has been lost for a wrong reason.
+reclassify_merged.owl: reclassify.owl
+	$(ROBOT) remove -i reclassify.owl --select imports -o $@
+
+o1_merged.owl: $(O1)
+	$(ROBOT) remove -i $(O1) --select imports -o $@
+
+tmp/types.owl: $(O1)
+	$(ROBOT) query -i $(O1) --query sparql/efo-types.ru $@
+
+unmerged.owl: tmp/types.owl reclassify_merged.owl o1_merged.owl
+	$(ROBOT) unmerge -i o1_merged.owl -i reclassify_merged.owl \
+		merge -i tmp/types.owl -o $@
+
+tmp/lost.owl: unmerged.owl
+	$(ROBOT) filter -i $< -T $(TERMLIST) --select complement --select classes --trim false \
+		convert -f ofn -o $@
+
+mv_efo:
+	$(ROBOT) convert -i reclassify.owl -f ofn -o efo-edit.owl
+
+sed:
+	sed -i 's/obo1:/obo2:/g' efo-edit.owl
+	sed -i 's/chebi5:/chebi6:/g' efo-edit.owl
+	sed -i 's/chebi4:/chebi5:/g' efo-edit.owl
+	sed -i 's/chebi3:/chebi4:/g' efo-edit.owl
+	sed -i 's/chebi2:/chebi3:/g' efo-edit.owl
+

src/ontology/sparql/efo_measurement.sparql

@@ -0,0 +1,14 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
+prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX EFO: <http://www.ebi.ac.uk/efo/EFO_>
+
+SELECT ?cls WHERE {
+	?cls a owl:Class .
+	?cls rdfs:subClassOf* EFO:0001444 .
+	FILTER NOT EXISTS {?cls owl:deprecated ?dep}
+	FILTER (!isBlank(?cls))
+}
+ORDER BY ?cls

src/ontology/sparql/oba-labels-to-synonym.ru

@@ -0,0 +1,36 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
+prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX EFO: <http://www.ebi.ac.uk/efo/EFO_>
+
+DELETE {
+	?cls rdfs:label ?label .
+	?cls oboInOwl:id ?oid .
+}
+
+INSERT {
+	?cls a owl:Class .
+  	?cls oboInOwl:hasExactSynonym ?label .
+		?cls oboInOwl:hasDbXref ?curie .
+  [] a owl:Axiom ;
+   owl:annotatedSource ?cls ;
+   owl:annotatedProperty oboInOwl:hasExactSynonym ;
+   owl:annotatedTarget ?label ;
+   rdfs:comment "OBA preferred label 06.07.2022." ;
+	 oboInOwl:hasDbXref ?curie .
+
+}
+
+WHERE {
+	?cls a owl:Class .
+	?cls rdfs:label ?label .
+	OPTIONAL {
+		?cls oboInOwl:id ?oid .
+	}
+	FILTER NOT EXISTS {?cls owl:deprecated ?dep}
+	FILTER (isIRI(?cls) && regex(str(?cls), "^http://purl.obolibrary.org/obo/OBA_"))
+	FILTER (!isBlank(?cls))
+	BIND(REPLACE(?cls, "http://purl.obolibrary.org/obo/OBA_", "OBA:", "i") AS ?curie)
+}