Stream: genomics/committers
Topic: External CodeSystem Updates
Patrick Werner (Apr 02 2022 at 13:39):
I'm currently creating issues for HTA for missing SIDs of external CS in our IG.
Patrick Werner (Apr 02 2022 at 13:40):
- ClinVar Accession ID (RCV)(NCBI/NLM): Codes are starting with RCV -> can be distinguished from Variant IDs. If needed, a VS with a filter can be created. -> NO HTA Issue, should be removed from http://build.fhir.org/ig/HL7/genomics-reporting/codings.html
Patrick Werner (Apr 02 2022 at 13:49):
- Chromloc Location: https://jira.hl7.org/browse/HTA-81
Patrick Werner (Apr 02 2022 at 13:52):
- dbVar - Germline -> will ask HTA for a SID for the whole dbVar CS, Germline vs. Somatic can be handled by a VS
https://jira.hl7.org/browse/HTA-82
Patrick Werner (Apr 02 2022 at 13:58):
- Gene Code (NCBI/NLM) https://jira.hl7.org/browse/HTA-83
Kevin Power (Apr 02 2022 at 13:58):
Thanks Patrick!
RE ClinVar Accessions. I know it was suggested to not use allele ids but now that I think about it I am not sure about accessions?
Patrick Werner (Apr 02 2022 at 14:01):
Kevin Power said:
Thanks Patrick!
RE ClinVar Accessions. I know it was suggested to not use allele ids but now that I think about it I am not sure about accessions?
I see Clinvar as a single CS, currently without an agreed CS.url. This is not about suggesting usage or not i think.
BUT: i removed the line from the table in a local branch, so we don' "advertise" the usage.
Kevin Power (Apr 02 2022 at 14:02):
Got ya. That makes sense to me.
Patrick Werner (Apr 02 2022 at 14:03):
- GLSTRING: https://jira.hl7.org/browse/HTA-84
Patrick Werner (Apr 02 2022 at 14:12):
- HPO (already requested): https://jira.hl7.org/browse/HTA-25
Kevin Power (Apr 02 2022 at 14:14):
We probably need to collect all these on a confluence page or something similar?
Patrick Werner (Apr 02 2022 at 14:14):
I don't know will point to this thread, but i can copy this to confluence as well.
Patrick Werner (Apr 02 2022 at 14:19):
- Pharmvar Star Allele: https://jira.hl7.org/projects/HTA/issues/HTA-85
Joel Schneider (Apr 04 2022 at 04:17):
Thanks Patrick.
CG also has some other HTA tickets currently "in progress" or "submitted".
https://jira.hl7.org/browse/HTA-65 ISCN code system - "system" uri ***
https://jira.hl7.org/browse/HTA-67 Adding Genotype Ontology (GENO)
https://jira.hl7.org/browse/HTA-68 Adding SEPIO-CG
https://jira.hl7.org/browse/HTA-69 Adding CLINVAR-RS
https://jira.hl7.org/browse/HTA-70 Adding PGKB-ClinAnnLevels
https://jira.hl7.org/browse/HTA-71 HGNC Codesystem needs to be splitted
*** terminology.hl7.org (THO) already has a page for ISCN, so I'm not sure why the HTA-65 status is still "in progress"
They haven't posted an agenda yet, but I expect the next HTA meeting will be this Thursday, April 7, at 13:00 UTC (08:00 CDT). I was planning to ask them to prioritize HTA-71.
Joel Schneider (Apr 07 2022 at 14:21):
We discussed the HGNC ticket at today's HTA meeting.
https://jira.hl7.org/browse/HTA-71 HGNC Codesystem needs to be splitted
It was noted that a HGNC code system URL is listed in the FHIR R4 spec ("it SHALL be used"), which complicates the discussion.
The HTA would like to discuss the topic directly with a HGNC representative at some future HTA meeting. My understanding is that we are already in contact with HGNC. Would it be possible for us to invite someone from HGNC to attend a future HTA meeting?
Kevin Power (Apr 10 2022 at 14:43):
I think @ Bob Milius has a HGNC contact. Or, at worst case, could reach out to the email here:
https://www.genenames.org/contact/
Last updated: Apr 12 2022 at 19:14 UTC
