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 |
<ConceptMap xmlns="http://hl7.org/fhir">
<id value="GMSWGSGuideHPOTermsToSCT"/>
<language value="en"/>
<text>
<status value="generated"/>
<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>
</text>
<url
value="https://fhir.nwgenomics.nhs.uk/ConceptMap/GMSWGSGuideHPOTermsToSCT"/>
<version value="2.2.0"/>
<name value="GMSWGSGuideHPOTermsToSCT"/>
<title value="GMS WGS Guide HPO Terms to SNOMED CT"/>
<status value="draft"/>
<experimental value="true"/>
<date value="2026-09-20T05:53:36+00:00"/>
<publisher value="NHS North West Genomics"/>
<contact>
<telecom>
<system value="url"/>
<value value="https://www.nwgenomics.nhs.uk/contact-us"/>
</telecom>
</contact>
<description
value="HPO (Human Phenotype Ontology) to SNOMED CT mapping for the 38 terms in
[GMSWGSGuideHPOTermsVS](ValueSet-GMSWGSGuideHPOTermsVS.html) - see
[Questionnaire-GMSWGSRareDisease](Questionnaire-GMSWGSRareDisease.html)'s
`NOS/HPOTerm` item.
Built against the Genomics England terminology server
(https://re-docs.genomicsengland.co.uk/terminology_server/,
`https://ontoserver.aws.gel.ac/fhir`), HPO release `20191108`. That server
only publishes a **SNOMED CT to HPO** `ConceptMap` (`sct-to-hpo`) by name,
but does support querying it in the HPO-to-SNOMED direction directly via
`ConceptMap/sct-to-hpo/$translate?...&reverse=true` - see [nw-gmsa/Testing
notebook 13](https://github.com/nw-gmsa/Testing/blob/main/notebooks/13-snomed-to-hpo-genomic-clinical-indication.ipynb),
which uses the same server and surfaced this parameter. An initial pass of
this ConceptMap missed that: it instead found a candidate SNOMED CT concept
for each HPO term (`ValueSet/$expand` free-text search under the Clinical
finding (`404684003`) subtree) and forward-verified it through
`ConceptMap/sct-to-hpo/$translate` in the SNOMED-to-HPO direction - which
undercounted, since a genuinely-mapped HPO term can have a mapped SNOMED
code that isn't the one a text search happens to surface (e.g. Cataract
*is* mapped, to SNOMED `128306009`, not the `193570009` a plain text search
returns first). This version instead queries `reverse=true` directly for
every HPO code, with the `equivalence` value taken directly from that
server response (`equivalent` in every case found).
**27 of the 38 terms resolved this way; the remaining 11 do not appear in
the server's `sct-to-hpo` map even via `reverse=true`** - so these are
genuinely absent from the server's curated map, not an artefact of the
search methodology. Rather than assert an unverified equivalence,
unresolved terms are recorded below with `equivalence = unmatched` and no
target code."/>
<jurisdiction>
<coding>
<system value="urn:iso:std:iso:3166"/>
<code value="GB"/>
<display value="United Kingdom of Great Britain and Northern Ireland"/>
</coding>
</jurisdiction>
<sourceUri value="http://purl.obolibrary.org/obo/hp.owl"/>
<group>
<source value="http://purl.obolibrary.org/obo/hp.owl"/>
<sourceVersion value="20191108"/>
<target value="http://snomed.info/sct"/>
<targetVersion
value="http://snomed.info/sct/83821000000107/version/20240605"/>
<element>
<code value="HP:0001639"/>
<target>
<code value="233873004"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001644"/>
<target>
<code value="399020009"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001638"/>
<target>
<code value="85898001"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0002721"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0040088"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0005368"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0012647"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0000518"/>
<target>
<code value="128306009"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0000556"/>
<target>
<code value="314407005"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0007754"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0005562"/>
<target>
<code value="253883006"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001407"/>
<target>
<code value="85057007"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0002342"/>
<target>
<code value="61152003"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0002187"/>
<target>
<code value="31216003"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0010864"/>
<target>
<code value="40700009"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001263"/>
<target>
<code value="224958001"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001290"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0001508"/>
<target>
<code value="54840006"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001999"/>
<target>
<code value="112630007"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001939"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0000252"/>
<target>
<code value="1829003"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0000256"/>
<target>
<code value="19410003"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0000098"/>
<target>
<code value="248328003"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0004322"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0002652"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0000365"/>
<target>
<code value="15188001"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0003560"/>
<target>
<code value="73297009"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0003198"/>
<target>
<code value="129565002"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0002486"/>
<target>
<code value="3434004"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0009830"/>
<target>
<code value="302226006"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0100543"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0001257"/>
<target>
<code value="221360009"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0002072"/>
<target>
<equivalence value="unmatched"/>
</target>
</element>
<element>
<code value="HP:0001332"/>
<target>
<code value="15802004"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001251"/>
<target>
<code value="20262006"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001272"/>
<target>
<code value="95646004"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001321"/>
<target>
<code value="16026008"/>
<equivalence value="equivalent"/>
</target>
</element>
<element>
<code value="HP:0001250"/>
<target>
<code value="91175000"/>
<equivalence value="equivalent"/>
</target>
</element>
</group>
</ConceptMap>