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Snomed mapping analysis draft #10389

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Snomed mapping analysis draft #10389

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8 changes: 8 additions & 0 deletions src/ontology/config/hp-snomed.sssom.yml
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@@ -0,0 +1,8 @@
license: "https://creativecommons.org/publicdomain/zero/1.0/"
mapping_set_id: http://purl.obolibrary.org/obo/hp/mappings/hp-snomed
curie_map:
rdfs: "http://www.w3.org/2000/01/rdf-schema#"
owl: "http://www.w3.org/2002/07/owl#"
SNOMED: "http://snomed.info/id/"
HP: http://purl.obolibrary.org/obo/HP_
orcid: "https://orcid.org/"
14 changes: 14 additions & 0 deletions src/ontology/config/inverse-map.yml
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inverse_predicate_map:
skos:closeMatch: skos:closeMatch
skos:relatedMatch: skos:relatedMatch
skos:exactMatch: skos:exactMatch
skos:narrowMatch: skos:broadMatch
skos:broadMatch: skos:narrowMatch
semapv:crossSpeciesExactMatch: semapv:crossSpeciesExactMatch
semapv:crossSpeciesNarrowMatch: semapv:crossSpeciesBroadMatch
semapv:crossSpeciesBroadMatch: semapv:crossSpeciesNarrowMatch
semapv:crossSpeciesCloseMatch: semapv:crossSpeciesCloseMatch
owl:equivalentClass: owl:equivalentClass
owl:sameAs: owl:sameAs
rdfs:subClassOf: sssom:superClassOf
sssom:superClassOf: rdfs:subClassOf
3 changes: 2 additions & 1 deletion src/ontology/config/prefixes.csv
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Expand Up @@ -227,4 +227,5 @@ ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/
ICD10WHO,https://icd.who.int/browse10/2019/en#/
OMIMPS,https://omim.org/phenotypicSeries/PS
OMIM,https://omim.org/entry/
Orphanet,http://www.orpha.net/ORDO/Orphanet_
Orphanet,http://www.orpha.net/ORDO/Orphanet_
SNOMED, http://snomed.info/id/
27 changes: 27 additions & 0 deletions src/ontology/hp.Makefile
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Expand Up @@ -577,3 +577,30 @@ $(TMPDIR)/hp-%-merged.owl: hp-base.owl tmp/%.owl

mappings:
$(MAKE_FAST) ../mappings/hp-snomed.lexmatch.sssom.tsv

SNOMED_HPO=https://docs.google.com/spreadsheets/d/e/2PACX-1vTHNmZFJJ0zExDORNE1rekVfeSny1Bv5_q6XXAFeuBkLHbeucokTPvjuTBZlRUbHyuAm26PQlzkMBAH/pub?gid=488628125&single=true&output=tsv
tmp/hp-snomed-external.sssom.tsv:
wget "$(SNOMED_HPO)" -O $@

tmp/hp-snomed.sssom.tsv: tmp/hp-snomed-external.sssom.tsv
sssom parse $< -m config/hp-snomed.sssom.yml -o $@

tmp/snomed-hp.sssom.tsv: tmp/hp-snomed.sssom.tsv
sssom invert $< --inverse-map config/inverse-map.yml -o $@

tmp/snomed-hp.sssom.ttl: tmp/snomed-hp.sssom.tsv
sssom convert $< -O owl -o $@

tmp/snomed.owl: tmp/snomed-hp.sssom.ttl
$(ROBOT) merge -i tmp/snomed-0324.owl -i tmp/hp-snomed.sssom.ttl convert -f owl -o $@

tmp/hp-snomed.basic-validation.txt: tmp/snomed.db
runoak -i $< validate-mappings -o $@

tmp/hp-snomed.llm-validation.txt: tmp/snomed.db hp.obo
runoak -i llm:$< validate-mappings --adapter-mapping hp=hp.obo > $@

validate-mappings:
make IMP=false MIR=false PAT=false tmp/hp-snomed.basic-validation.txt
make IMP=false MIR=false PAT=false tmp/hp-snomed.llm-validation.txt

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