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Add method to ensure that hpoa annos are converted to Mondo first #930

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Add method to ensure that hpoa annos are converted to Mondo first #930

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55a383e
Add method to ensure that hpoa annos are converted to Mondo first
matentzn Jan 7, 2021
4da1444
Update Makefile
matentzn Jan 7, 2021
68630f5
Update .gitignore
matentzn Jan 7, 2021
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -44,3 +44,4 @@ src/ontology/components/legal_diseases.txt
src/ontology/components/d2p_*.ttl
src/ontology/components/disease_to_phenotype_merged_signature.tsv
src/ontology/components/efo-rename.tsv
src/ontology/components/mondo-rename.tsv
7 changes: 6 additions & 1 deletion src/ontology/Makefile
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Expand Up @@ -148,6 +148,10 @@ components/d2p_%.ttl: mirror/%.owl

components/efo-rename.tsv: components/mondo_efo_mappings.tsv components/disease_to_phenotype_merged_signature.tsv
python3 ../scripts/rename_tsv_subset.py $^ $@

components/mondo-rename.tsv: mirror/mondo.owl
$(ROBOT) query -i $< -q $(SPARQLDIR)/mondo_rename.sparql $@
cat $@ | tr -d '<>,' > [email protected] && mv [email protected] $@

# If you change the relation in the sparql query, make sure you add the new relation here as well.
components/legal_diseases.txt: $(SRC) components/disease_to_phenotype_merged.owl
Expand All @@ -164,8 +168,9 @@ components/disease_to_phenotype_merged.owl: $(D2P_RAW)
$(ROBOT) merge $(addprefix -i , $(D2P_RAW)) \
annotate --ontology-iri "http://www.ebi.ac.uk/efo/$@" -o $@

components/disease_to_phenotype.owl: components/disease_to_phenotype_merged.owl components/efo-rename.tsv components/legal_diseases.txt
components/disease_to_phenotype.owl: components/disease_to_phenotype_merged.owl components/mondo-rename.tsv components/efo-rename.tsv components/legal_diseases.txt
$(ROBOT) merge -i $< \
rename --mappings components/mondo-rename.tsv \
rename --mappings components/efo-rename.tsv \
remove -T components/legal_diseases.txt --select complement --trim true \
query --update $(SPARQLDIR)/remove-stray-classes.ru \
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17 changes: 17 additions & 0 deletions src/sparql/mondo_rename.sparql
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@@ -0,0 +1,17 @@
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dbpedia2: <http://dbpedia.org/property/>
PREFIX dbpedia: <http://dbpedia.org/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?source ?mondo
WHERE {
{ ?mondo skos:exactMatch ?source . }
FILTER(isIRI(?mondo) && (regex(str(?mondo), "http://purl.obolibrary.org/obo/MONDO_")))
}