FHIR Chat · how to use HGNC valueset? · genomics

Stream: genomics

Topic: how to use HGNC valueset?

Bob Milius (Mar 20 2020 at 21:01):

So I'm looking at http://hl7.org/fhir/uv/genomics-reporting/STU1/valueset-hgnc.html and I'm trying to understand how to use it. It says

    Include all codes defined in http://www.genenames.org/geneId
    Include all codes defined in http://www.genenames.org/genegroup

If I create an instance of an Observation.component[gene-studied].valueCodeableConcept, do I have to use one of those urls as the system? or can I use http://www.genenames.org, e.g.,

"valueCodeableConcept": {
        "coding": [
          {
            "code": "HGNC:4931",
            "system": "http://www.genenames.org"
          }
        ]
      }

vs

"valueCodeableConcept": {
        "coding": [
          {
            "code": "HGNC:4931",
            "system": "http://www.genenames.org/geneId"
          }
        ]
      }

Are there any special considerations if I create another valueset for another constrained profile that includes only a select subset of HGNC?

Kevin Power (Mar 21 2020 at 16:13):

I have to admit I don't know for sure, but am fairly confident you will want to use "../geneId" - but at this point, I don't know that it would be causing any of the errors you are seeing, since we don't really have support for HGNC codes.

Patrick Werner (Mar 22 2020 at 12:13):

i already replied in the other thread:
Patrick Werner 13:11
hi @ Bob Milius the correct uri of a gene id instance would be:

"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org/geneId",
"code": "HGNC:4931"
}

Patrick Werner (Mar 22 2020 at 12:33):

i just uploaded the hgnc CS & VS which is used by Molit internally: https://cloud.echinos.eu/index.php/s/gjj9dxsGYtWafJX

Last updated: Apr 12 2022 at 19:14 UTC