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fix: override ICD10CM canonical prefix to use purl.bioontology.org #80

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fix: override ICD10CM canonical prefix to use purl.bioontology.org #80

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1b84ff6
fix ICD10CM canonical prefix to use purl.bioontology.org
kevinschaper Feb 19, 2026
f6d8f92
refresh poetry.lock to fix CI dependency resolution
kevinschaper Feb 20, 2026
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90 changes: 80 additions & 10 deletions poetry.lock
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7 changes: 7 additions & 0 deletions src/prefixmaps/data/go.csv
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Expand Up @@ -10,6 +10,7 @@ go,CL,http://purl.obolibrary.org/obo/CL_,canonical
go,dbSNP,http://identifiers.org/dbsnp/,canonical
go,DDANAT,http://purl.obolibrary.org/obo/DDANAT_,canonical
go,dictyBase,http://identifiers.org/dictybase.gene/,canonical
go,EC,http://purl.uniprot.org/enzyme/,canonical
go,ECO,http://purl.obolibrary.org/obo/ECO_,canonical
go,EMAPA,http://purl.obolibrary.org/obo/EMAPA_,canonical
go,ENSEMBL,http://identifiers.org/ensembl/,canonical
Expand All @@ -31,6 +32,7 @@ go,IntAct,http://identifiers.org/intact/,canonical
go,InterPro,http://identifiers.org/interpro/,canonical
go,KEGG_ENZYME,http://identifiers.org/kegg.enzyme/,canonical
go,KEGG_PATHWAY,http://identifiers.org/kegg.pathway/,canonical
go,KEGG_REACTION,http://www.kegg.jp/entry/,canonical
go,MA,http://purl.obolibrary.org/obo/MA_,canonical
go,MaizeGDB_Locus,http://identifiers.org/maizegdb.locus/,canonical
go,MetaCyc,http://identifiers.org/metacyc.reaction/,canonical
Expand All @@ -46,16 +48,21 @@ go,PomBase,http://identifiers.org/pombase/,canonical
go,PR,http://purl.obolibrary.org/obo/PR_,canonical
go,Reactome,http://identifiers.org/reactome/,canonical
go,RGD,http://identifiers.org/rgd/,canonical
go,RHEA,http://rdf.rhea-db.org/,canonical
go,RO,http://purl.obolibrary.org/obo/RO_,canonical
go,SGD,http://identifiers.org/sgd/,canonical
go,SGN,http://identifiers.org/sgn/,canonical
go,SO,http://purl.obolibrary.org/obo/SO_,canonical
go,TAIR,http://identifiers.org/tair.locus/,canonical
go,TC,http://identifiers.org/tcdb/,canonical
go,TGD,http://identifiers.org/tgd/,canonical
go,TreeGrafter,http://identifiers.org/panther.family/,namespace_alias
go,TriTrypDB,http://identifiers.org/tritrypdb/,canonical
go,UBERON,http://purl.obolibrary.org/obo/UBERON_,canonical
go,UM-BBD_pathwayID,http://identifiers.org/umbbd.pathway/,canonical
go,UM-BBD_reactionID,http://identifiers.org/umbbd.reaction/,canonical
go,UniProtKB,http://identifiers.org/uniprot/,canonical
go,VZ,https://viralzone.expasy.org/,canonical
go,WB,http://identifiers.org/wormbase/,canonical
go,WBls,http://purl.obolibrary.org/obo/WBls_,canonical
go,WBPhenotype,http://purl.obolibrary.org/obo/WBPhenotype_,canonical
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1 change: 1 addition & 0 deletions src/prefixmaps/data/linked_data.csv
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Expand Up @@ -3,6 +3,7 @@ linkml,bibo,http://purl.org/ontology/bibo/,canonical
linkml,biolink,https://w3id.org/biolink/vocab/,canonical
linkml,dcterms,http://purl.org/dc/terms/,canonical
linkml,foaf,http://xmlns.com/foaf/0.1/,canonical
linkml,ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,canonical
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@matentzn matentzn Feb 20, 2026

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I am not against this, note that Bioregistrysuggests this:

https://www.icd10data.com/search?s=

Which is a bit of a hack - redirecting to the search page rather than the concept page for which you cant construct a URI.

linkml,linkml,https://w3id.org/linkml/,canonical
linkml,NANDO,http://identifiers.org/NANDO:,canonical
linkml,NCIThesaurus,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#,canonical
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1 change: 1 addition & 0 deletions src/prefixmaps/data/linked_data.curated.yaml
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Expand Up @@ -24,5 +24,6 @@ prefixes:
biolink: https://w3id.org/biolink/vocab/
foaf: http://xmlns.com/foaf/0.1/
NANDO: "http://identifiers.org/NANDO:"
ICD10CM: "http://purl.bioontology.org/ontology/ICD10CM/"


86 changes: 59 additions & 27 deletions src/prefixmaps/data/merged.csv
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86 changes: 59 additions & 27 deletions src/prefixmaps/data/merged.monarch.csv
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86 changes: 59 additions & 27 deletions src/prefixmaps/data/merged.oak.csv
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1 change: 1 addition & 0 deletions src/prefixmaps/data/obo.csv
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Expand Up @@ -186,6 +186,7 @@ obo,ORNASEQ,http://purl.obolibrary.org/obo/ORNASEQ_,canonical
obo,OVAE,http://purl.obolibrary.org/obo/OVAE_,canonical
obo,PAO,http://purl.obolibrary.org/obo/PAO_,canonical
obo,PATO,http://purl.obolibrary.org/obo/PATO_,canonical
obo,PBPKO,http://purl.obolibrary.org/obo/PBPKO_,canonical
obo,PCL,http://purl.obolibrary.org/obo/PCL_,canonical
obo,PCO,http://purl.obolibrary.org/obo/PCO_,canonical
obo,PD_ST,http://purl.obolibrary.org/obo/PD_ST_,canonical
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63 changes: 47 additions & 16 deletions src/prefixmaps/data/prefixcc.csv
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116 changes: 115 additions & 1 deletion src/prefixmaps/data/w3id.csv
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