NHS North West Genomics
2.2.0 - ci-build
NHS North West Genomics
2.2.0 - ci-build
NHS North West Genomics - Local Development build (v2.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
| Draft as of 2026-09-20 |
{
"resourceType" : "ConceptMap",
"id" : "GMSWGSGuideHPOTermsToSCT",
"language" : "en",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: ConceptMap GMSWGSGuideHPOTermsToSCT</b></p><a name=\"GMSWGSGuideHPOTermsToSCT\"> </a><a name=\"hcGMSWGSGuideHPOTermsToSCT\"> </a><p>Mapping from http://purl.obolibrary.org/obo/hp.owl to (not specified)</p><br/><p>Mapping from <code>http://purl.obolibrary.org/obo/hp.owl|20191108</code> to <code>http://snomed.info/sct|http://snomed.info/sct/83821000000107/version/20240605</code></p><table class=\"grid\"><tr><td><b>Source Code</b></td><td><b>Relationship</b></td><td><b>Target Code</b></td></tr><tr><td>HP:0001639</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>233873004</td></tr><tr><td>HP:0001644</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>399020009</td></tr><tr><td>HP:0001638</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>85898001</td></tr><tr><td>HP:0002721</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0040088</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0005368</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0012647</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0000518</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>128306009</td></tr><tr><td>HP:0000556</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>314407005</td></tr><tr><td>HP:0007754</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0005562</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>253883006</td></tr><tr><td>HP:0001407</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>85057007</td></tr><tr><td>HP:0002342</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>61152003</td></tr><tr><td>HP:0002187</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>31216003</td></tr><tr><td>HP:0010864</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>40700009</td></tr><tr><td>HP:0001263</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>224958001</td></tr><tr><td>HP:0001290</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0001508</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>54840006</td></tr><tr><td>HP:0001999</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>112630007</td></tr><tr><td>HP:0001939</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0000252</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>1829003</td></tr><tr><td>HP:0000256</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>19410003</td></tr><tr><td>HP:0000098</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>248328003</td></tr><tr><td>HP:0004322</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0002652</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0000365</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>15188001</td></tr><tr><td>HP:0003560</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>73297009</td></tr><tr><td>HP:0003198</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>129565002</td></tr><tr><td>HP:0002486</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>3434004</td></tr><tr><td>HP:0009830</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>302226006</td></tr><tr><td>HP:0100543</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0001257</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>221360009</td></tr><tr><td>HP:0002072</td><td colspan=\"2\" style=\"background-color: #efefef\">(not mapped)</td></tr><tr><td>HP:0001332</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>15802004</td></tr><tr><td>HP:0001251</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>20262006</td></tr><tr><td>HP:0001272</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>95646004</td></tr><tr><td>HP:0001321</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>16026008</td></tr><tr><td>HP:0001250</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#concept-map-equivalence-equivalent\" title=\"equivalent\">is equivalent to</a></td><td>91175000</td></tr></table></div>"
},
"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"
}
]
}
]
}
]
}