cancerDHC/ccdhmodel

support forming a URI from Coding values

Opened this issue · 2 comments

balhoff commented

Currently an instance of Coding looks like this:

collection_site:                                            # type = BodySite
    site:                                                     # type = CodeableConcept
      coding:                                                 # type = Coding
        - code: C12468
          label: Lung
          system: http://ncithesaurus.nci.nih.gov
          tag:
            - harmonized
        - code: Lung
          label: Lung
          system: http://crdc.nci.nih.gov/gdc
          tag:
            - original

While the system value is a URI, this doesn't imply that it can be used as a URI namespace to be prepended to the code, if one wants to derive a URI for the coding value to use in RDF-based tools. In FHIR examples I've seen, this URI is not intended to be a namespace, just an identifier for a system. It would be nice if CRDC-H (or even as a feature of LinkML) we had a defined way to include a URI version of the coding value, or generate a URI from components in the coding instance. If we are going to use the CodeableConcept model, I don't think we need to precisely mirror FHIR. We could support better interoperability with the linked data world.

bfurner commented

I'm not sure I'm totally following the nuances here, so we should discuss at an upcoming meeting.

What we are looking to support in a Coding are 1) the code, 2) ideally a resolvable URL to an authoritative source for the code system, and 3) a version of the code system from which the code is drawn. In these examples, we're only showing the code and system, but certainly would want the flexibility to support versioning.

I take it you would like to see support for the 'code' represented as a CURIE (e.g. NCIT:C12468) as well as the simple code (e.g. C12468)?

balhoff commented

I take it you would like to see support for the 'code' represented as a CURIE (e.g. NCIT:C12468) as well as the simple code (e.g. C12468)?

Yes, basically a predictable way to interoperate with semantic web tools, where an identifier is expected to be a URI.