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Removing self-xrefs from release #1665

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Removing self-xrefs from release #1665

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9b7c5b7
Added inject-subclass-declaration to OWL file
zoependlington Jul 8, 2022
e28c11b
Updated Makefile and sparql queries for removing self xrefs
zoependlington Jul 8, 2022
acd446c
Update remove-internal-xrefs.sparql
matentzn Jul 8, 2022
de9a501
Updates
matentzn Jul 8, 2022
495e2d5
Update remove-internal-xrefs.sparql
matentzn Jul 8, 2022
27c4999
Update remove-internal-xrefs.sparql
matentzn Jul 8, 2022
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4 changes: 3 additions & 1 deletion src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -257,12 +257,14 @@ release: $(BUILDDIR)/$(ONT).owl $(BUILDDIR)/$(ONT).obo $(BUILDDIR)/$(ONT).json $

$(BUILDDIR)/$(ONT).owl: $(SRC)
$(ROBOT) merge -i $< \
query \
--update ../sparql/inject-subset-declaration.sparql \
--update ../sparql/remove-internal-xrefs.sparql \
reason -s true -m false -r hermit \
annotate -a owl:versionInfo `cat version.txt` -a rdfs:comment `date +%Y-%m-%d` -O $(BASE)/$(ONT).owl -V $(BASE)/releases/v`cat version.txt`/$(ONT).owl -o $@

$(BUILDDIR)/$(ONT).obo: $(BUILDDIR)/$(ONT).owl
$(ROBOT) annotate -i $< --ontology-iri http://www.ebi.ac.uk/efo/efo.owl --version-iri http://www.ebi.ac.uk/efo/releases/v`cat version.txt`/efo.owl \
query --update ../sparql/inject-subset-declaration.sparql \
convert --check false -f obo -o $@

$(BUILDDIR)/$(ONT).json: $(BUILDDIR)/$(ONT).owl
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51 changes: 51 additions & 0 deletions src/sparql/remove-internal-xrefs.sparql
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@@ -0,0 +1,51 @@
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 oio: <http://www.geneontology.org/formats/oboInOwl#>

DELETE {
?axiom owl:annotatedSource ?cls ;
owl:annotatedProperty oio:hasDbXref ;
owl:annotatedTarget ?obj_curie ;
?x ?y .
?cls oio:hasDbXref ?obj_curie .
}
#SELECT DISTINCT ?cls ?obj_curie ?obj_iri
WHERE {
?cls a owl:Class ;
oio:hasDbXref ?obj_curie .

FILTER(REGEX(STR(?obj_curie),"^(GO|DOID|Orphanet|HP|MONDO|EFO):[0-9A-Za-z]+") || isURI(?obj_curie))

BIND(
URI(
IF(isURI(?obj_curie), ?obj_curie, REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(?obj_curie,
"GO:","http://purl.obolibrary.org/obo/GO_"),
"DOID:","http://purl.obolibrary.org/obo/DOID_"),
"Orphanet:","http://www.orpha.net/ORDO/Orphanet_"),
"HP:","http://purl.obolibrary.org/obo/HP_"),
"MONDO:","http://purl.obolibrary.org/obo/MONDO_"),
"EFO:","http://www.ebi.ac.uk/efo/EFO_")
)) as ?obj_iri)

OPTIONAL {
?axiom owl:annotatedSource ?cls ;
owl:annotatedProperty oio:hasDbXref ;
owl:annotatedTarget ?obj_curie ;
?x ?y .
OPTIONAL {
?axiom ?x1 ?y1 .
FILTER(?y!=?y1)
OPTIONAL {
?axiom ?x2 ?y2 .
FILTER(?y2!=?y1)
OPTIONAL {
?axiom ?x3 ?y3 .
FILTER(?y2!=?y3)
}
}
}
}

?obj_iri a owl:Class . ##<---TODO
}