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cancerDHC / ccdhmodel

CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
https://cancerdhc.github.io/ccdhmodel/
BSD 3-Clause "New" or "Revised" License
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support forming a URI from Coding values #129

Open balhoff opened 2 years ago

balhoff commented 2 years ago

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 2 years ago

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 2 years ago

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.