cancerDHC/example-data

Ongoing discussion about where to find mappings for terms as well as values

turbomam opened this issue · 4 comments

turbomam commented

I checked via_terminology_server.ipynb into this repo's issue-27-codable-concept-notebooks branch and created PR #28

I had two goals:

  • reimplement the GDC to CRDC-H Diagnosis conversions in GDC to CCDH conversion.ipynb to use codeable concepts instead of enumerations
  • uncouple mapping knowledge from executable code by using the CCDH terminology server. I would say that's going well for body sites and cancer stage observation values, but not for cancer stage observation types. The conversion of the GDC cancer stage observation types is currently hardcode as a bunch of if statements. I don't see how to look those up with the terminology server.
turbomam commented

Link for terminology server: https://terminology.ccdh.io

turbomam commented

Is there an issue anywhere for improving the terminology server's documentation? I know I've heard @joeflack4 talk about that and I would be glad to help.

gaurav commented

I think those are covered by:

joeflack4 commented

There's a link to this from the GitHub home page:
https://github.com/cancerDHC/ccdh-terminology-service/blob/master/docs/rest_api.md

Only so much can fit into the swagger docs. I think I need to add more. But at least there are descriptions there now for each endpoint: https://terminology.ccdh.io/docs#

I'm still wanting to add more documentation though. Here's what I plan on adding: cancerDHC/ccdh-terminology-service#118

If you have other suggestions for what the docs should include, feel free to add there.