{ "resourceType" : "ConceptMap", "id" : "GMSWGSGuideHPOTermsToSCT", "language" : "en", "text" : { "status" : "generated", "div" : "

Generated Narrative: ConceptMap GMSWGSGuideHPOTermsToSCT

Mapping from http://purl.obolibrary.org/obo/hp.owl to (not specified)


Mapping from http://purl.obolibrary.org/obo/hp.owl|20191108 to http://snomed.info/sct|http://snomed.info/sct/83821000000107/version/20240605

Source CodeRelationshipTarget Code
HP:0001639is equivalent to233873004
HP:0001644is equivalent to399020009
HP:0001638is equivalent to85898001
HP:0002721(not mapped)
HP:0040088(not mapped)
HP:0005368(not mapped)
HP:0012647(not mapped)
HP:0000518is equivalent to128306009
HP:0000556is equivalent to314407005
HP:0007754(not mapped)
HP:0005562is equivalent to253883006
HP:0001407is equivalent to85057007
HP:0002342is equivalent to61152003
HP:0002187is equivalent to31216003
HP:0010864is equivalent to40700009
HP:0001263is equivalent to224958001
HP:0001290(not mapped)
HP:0001508is equivalent to54840006
HP:0001999is equivalent to112630007
HP:0001939(not mapped)
HP:0000252is equivalent to1829003
HP:0000256is equivalent to19410003
HP:0000098is equivalent to248328003
HP:0004322(not mapped)
HP:0002652(not mapped)
HP:0000365is equivalent to15188001
HP:0003560is equivalent to73297009
HP:0003198is equivalent to129565002
HP:0002486is equivalent to3434004
HP:0009830is equivalent to302226006
HP:0100543(not mapped)
HP:0001257is equivalent to221360009
HP:0002072(not mapped)
HP:0001332is equivalent to15802004
HP:0001251is equivalent to20262006
HP:0001272is equivalent to95646004
HP:0001321is equivalent to16026008
HP:0001250is equivalent to91175000
" }, "url" : "https://fhir.nwgenomics.nhs.uk/ConceptMap/GMSWGSGuideHPOTermsToSCT", "version" : "2.2.0", "name" : "GMSWGSGuideHPOTermsToSCT", "title" : "GMS WGS Guide HPO Terms to SNOMED CT", "status" : "draft", "experimental" : true, "date" : "2026-09-20T05:53:36+00:00", "publisher" : "NHS North West Genomics", "contact" : [{ "telecom" : [{ "system" : "url", "value" : "https://www.nwgenomics.nhs.uk/contact-us" }] }], "description" : "HPO (Human Phenotype Ontology) to SNOMED CT mapping for the 38 terms in\n[GMSWGSGuideHPOTermsVS](ValueSet-GMSWGSGuideHPOTermsVS.html) - see\n[Questionnaire-GMSWGSRareDisease](Questionnaire-GMSWGSRareDisease.html)'s\n`NOS/HPOTerm` item.\n\nBuilt against the Genomics England terminology server\n(https://re-docs.genomicsengland.co.uk/terminology_server/,\n`https://ontoserver.aws.gel.ac/fhir`), HPO release `20191108`. That server\nonly publishes a **SNOMED CT to HPO** `ConceptMap` (`sct-to-hpo`) by name,\nbut does support querying it in the HPO-to-SNOMED direction directly via\n`ConceptMap/sct-to-hpo/$translate?...&reverse=true` - see [nw-gmsa/Testing\nnotebook 13](https://github.com/nw-gmsa/Testing/blob/main/notebooks/13-snomed-to-hpo-genomic-clinical-indication.ipynb),\nwhich uses the same server and surfaced this parameter. An initial pass of\nthis ConceptMap missed that: it instead found a candidate SNOMED CT concept\nfor each HPO term (`ValueSet/$expand` free-text search under the Clinical\nfinding (`404684003`) subtree) and forward-verified it through\n`ConceptMap/sct-to-hpo/$translate` in the SNOMED-to-HPO direction - which\nundercounted, since a genuinely-mapped HPO term can have a mapped SNOMED\ncode that isn't the one a text search happens to surface (e.g. Cataract\n*is* mapped, to SNOMED `128306009`, not the `193570009` a plain text search\nreturns first). This version instead queries `reverse=true` directly for\nevery HPO code, with the `equivalence` value taken directly from that\nserver response (`equivalent` in every case found).\n\n**27 of the 38 terms resolved this way; the remaining 11 do not appear in\nthe server's `sct-to-hpo` map even via `reverse=true`** - so these are\ngenuinely absent from the server's curated map, not an artefact of the\nsearch methodology. Rather than assert an unverified equivalence,\nunresolved terms are recorded below with `equivalence = unmatched` and no\ntarget code.", "jurisdiction" : [{ "coding" : [{ "system" : "urn:iso:std:iso:3166", "code" : "GB", "display" : "United Kingdom of Great Britain and Northern Ireland" }] }], "sourceUri" : "http://purl.obolibrary.org/obo/hp.owl", "group" : [{ "source" : "http://purl.obolibrary.org/obo/hp.owl", "sourceVersion" : "20191108", "target" : "http://snomed.info/sct", "targetVersion" : "http://snomed.info/sct/83821000000107/version/20240605", "element" : [{ "code" : "HP:0001639", "target" : [{ "code" : "233873004", "equivalence" : "equivalent" }] }, { "code" : "HP:0001644", "target" : [{ "code" : "399020009", "equivalence" : "equivalent" }] }, { "code" : "HP:0001638", "target" : [{ "code" : "85898001", "equivalence" : "equivalent" }] }, { "code" : "HP:0002721", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0040088", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0005368", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0012647", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0000518", "target" : [{ "code" : "128306009", "equivalence" : "equivalent" }] }, { "code" : "HP:0000556", "target" : [{ "code" : "314407005", "equivalence" : "equivalent" }] }, { "code" : "HP:0007754", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0005562", "target" : [{ "code" : "253883006", "equivalence" : "equivalent" }] }, { "code" : "HP:0001407", "target" : [{ "code" : "85057007", "equivalence" : "equivalent" }] }, { "code" : "HP:0002342", "target" : [{ "code" : "61152003", "equivalence" : "equivalent" }] }, { "code" : "HP:0002187", "target" : [{ "code" : "31216003", "equivalence" : "equivalent" }] }, { "code" : "HP:0010864", "target" : [{ "code" : "40700009", "equivalence" : "equivalent" }] }, { "code" : "HP:0001263", "target" : [{ "code" : "224958001", "equivalence" : "equivalent" }] }, { "code" : "HP:0001290", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0001508", "target" : [{ "code" : "54840006", "equivalence" : "equivalent" }] }, { "code" : "HP:0001999", "target" : [{ "code" : "112630007", "equivalence" : "equivalent" }] }, { "code" : "HP:0001939", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0000252", "target" : [{ "code" : "1829003", "equivalence" : "equivalent" }] }, { "code" : "HP:0000256", "target" : [{ "code" : "19410003", "equivalence" : "equivalent" }] }, { "code" : "HP:0000098", "target" : [{ "code" : "248328003", "equivalence" : "equivalent" }] }, { "code" : "HP:0004322", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0002652", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0000365", "target" : [{ "code" : "15188001", "equivalence" : "equivalent" }] }, { "code" : "HP:0003560", "target" : [{ "code" : "73297009", "equivalence" : "equivalent" }] }, { "code" : "HP:0003198", "target" : [{ "code" : "129565002", "equivalence" : "equivalent" }] }, { "code" : "HP:0002486", "target" : [{ "code" : "3434004", "equivalence" : "equivalent" }] }, { "code" : "HP:0009830", "target" : [{ "code" : "302226006", "equivalence" : "equivalent" }] }, { "code" : "HP:0100543", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0001257", "target" : [{ "code" : "221360009", "equivalence" : "equivalent" }] }, { "code" : "HP:0002072", "target" : [{ "equivalence" : "unmatched" }] }, { "code" : "HP:0001332", "target" : [{ "code" : "15802004", "equivalence" : "equivalent" }] }, { "code" : "HP:0001251", "target" : [{ "code" : "20262006", "equivalence" : "equivalent" }] }, { "code" : "HP:0001272", "target" : [{ "code" : "95646004", "equivalence" : "equivalent" }] }, { "code" : "HP:0001321", "target" : [{ "code" : "16026008", "equivalence" : "equivalent" }] }, { "code" : "HP:0001250", "target" : [{ "code" : "91175000", "equivalence" : "equivalent" }] }] }] }