Stream: genomics
Topic: terminology to unified IG
Andrew Patterson (Mar 22 2018 at 03:40):
The terminologies -> code systems page has a good list of genomics code system canonical URLs. But I feel that this section should be expanded with some more details to enable good use of these code systems. For instance, I know from looking at examples that the coded value for HGNC is the id, and the display value is the gene name. But one could easily not pick up on that - and think perhaps the gene name is the code. There would be similar scope for misalignment in lots of the genetics code systems.
I'd love to see "Using [genomic codesystem] with FHIR" pages (ala 'using SNOMED with FHIR'). Is that on anyones radar? And where would that page live - does it live in the new unified genomics IG, or in the core where the terminologies are currently listed? Or should the list of genomics codesystems all move to the IG?
Grahame Grieve (Mar 22 2018 at 05:45):
it should be in the base spec, and I'll happily add stuff like that if people do the work to come to agreement - it can be hard to run it to the ground. @Joel Schneider
Andrew Patterson (Mar 22 2018 at 05:55):
I can see some of the ways codesystems have been used in some of the CG examples - but it is hard to know if these are just ad-hoc attempts at usage or something that was the process of agreement. (guessing the former). The CSIRO has some interest in getting some of these code systems into ontoserver - at which point aligning (or driving) an official 'right way' would be useful. @Michael Lawley @Alejandro Metke . HPO and HGNC at least?
Grahame Grieve (Mar 22 2018 at 05:56):
well, pretty much the right way is to work from one of the fully fleshed out pages - loinc or snomedct, and for a small group of users to adapt to the code system in question, and then forward to me to add to the spec. i'll eyeball it, cross check with vocab co-chairs, and then add it with a note about it's status
Kevin Power (Mar 22 2018 at 13:38):
You might have seen it, but I wanted to point to our new genomics reporting IG: http://build.fhir.org/ig/HL7/genomics-unified/index.html
The CG examples you are seeing in core today will be different with the new IG. Determining the right terminologies has started and we have ideas, but it needs some work to be honest, and certainly needs to be documented better. Perhaps @Lloyd McKenzie might have more to say.
Joel Schneider (Mar 22 2018 at 13:55):
I've done some exploration of how the official IMGT/HLA nomenclature could be used in a FHIR setting, as a (genomic) CodeSystem. However, that effort has been on the back burner for a while, and is due for a few revisions.
Preliminary artifacts produced so far include a proof-of-concept terminology service, and a code system bundle:
http://mac-and-fhir-prototype.us-east-1.elasticbeanstalk.com
https://s3.amazonaws.com/nmdp-fhir-terminology/who/fhir-imgt-hla-terminology-20170729.zip
I'd be happy to have comments or discussion on this stuff, and expect to revisit it during future connectathons (hopefully May).
Andrew Patterson (Mar 22 2018 at 22:50):
You might have seen it, but I wanted to point to our new genomics reporting IG: http://build.fhir.org/ig/HL7/genomics-unified/index.html
The CG examples you are seeing in core today will be different with the new IG.
Yes I have seen - your email about IG Review was what prompted my posting. Part of my question is related to whether the future work in the genomics terminology space (i.e better documentation) should be living in the Genomics IG or staying in the core. Grahame seems to be indicating that he is happy for it to stay in the core
Grahame Grieve (Mar 22 2018 at 22:55):
well, the general guidance is that if everyone has to follow it whatever , it should be in the core. And that's the case for using these code systems. - it isn't like 'you use it this way with the IG, otherwise, whatever'. No, there's only one way... and so it goes in core
Alejandro Metke (Mar 22 2018 at 22:55):
We'll start with HPO. I'll write the page once I'm done with the new transformation and send to Grahame for review.
Kevin Power (Mar 23 2018 at 13:54):
The IG we are building will be our recommendation. We are working on it outside of the core today, but based on guidance from FMG, we may end up publishing it as part of core by September. As you develop this of documentation @Alejandro Metke , we can work with you to review it and get it into our IG.
Alejandro Metke (Mar 26 2018 at 03:49):
That's great @Kevin Power. I'll keep you in the loop.
Bret H (Mar 29 2018 at 10:46):
what is the use case for HPO? please clarify?
Bret H (Mar 29 2018 at 10:49):
There was a person chosen as the CG WG vocab representative. Can't recall there name at the moment. Have they been involved?
Lloyd McKenzie (Mar 29 2018 at 14:16):
We haven't really done much with terminologies yet other than retaining mentions of the terminologies explicitly bound in the v2 space
Andrew Patterson (Apr 01 2018 at 23:01):
what is the use case for HPO? please clarify?
@Bret H our clinical users exchange HPO codes with the genomics lab (on test order) to narrow down the genes of interest. And we also want to record them against any genomic artifacts for later queries ('find me all the undiagnosed samples exhibiting abnormality of axial muscles')
The coverage of HPO overlaps with SNOMED but not enough for our users
Bret H (Jan 08 2019 at 17:05):
Thanks.
Bob Freimuth (Mar 06 2019 at 19:11):
HPO is open, SNOMED is not. HPO is gaining significant traction in GA4GH, lead by Melissa Haendel. While primarily used more on the research side, NCATS is looking at it for clinical/translational as well. I certainly wouldn't count it out.
Last updated: Apr 12 2022 at 19:14 UTC
