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Coding object in mappings is not being represented correctly #220

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korikuzma opened this issue Jan 17, 2025 · 0 comments · May be fixed by #221
Open

Coding object in mappings is not being represented correctly #220

korikuzma opened this issue Jan 17, 2025 · 0 comments · May be fixed by #221
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bug Something isn't working priority:high High priority

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@korikuzma
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Describe the bug

I had met with Alex to review CIViC assertion representation using the latest GKS ballot releases. During this review, he noted we should be representing Coding objects in mappings differently than what is stated by the descriptions.

Steps to reproduce

Go to https://normalize.cancervariants.org/disease/normalize?q=melanoma and look at mappings

Expected behavior

  • code must use syntax defined by the system (e.g. C3224)
  • system must use iriReference, not a free-text label
    • Priority for value used:
      1. systemPrefixExpansion: e.g. https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=
      2. specification
      3. homepage
  • id can be the concept_id (CURIE)

Current behavior

  • code is always using concept ID (CURIE)
  • system sometimes uses free-text label
  • No id field

Acceptance Criteria

Given I'm querying the /normalize endpoint,
When I'm accessing mappings,
Then code be the code syntax defined by the system, system should use iriReference, and id will be the concept_id

"coding": {
    "id": "ncit:C3224",
    "system": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=",
    "code": "C3224"
}

Possible reason(s)

No response

Suggested fix

No response

Branch, commit, and/or version

v0.7.0

Screenshots

No response

Environment details

NA

Additional details

No response

Contribution

Yes, I can create a PR for this fix.

@korikuzma korikuzma added bug Something isn't working priority:high High priority labels Jan 17, 2025
@korikuzma korikuzma self-assigned this Jan 17, 2025
korikuzma added a commit that referenced this issue Jan 18, 2025
close #220

* `system` MUST use `iriReference`, not a free-text label
* `code` MUST use syntax defined by the `system`
* `id` will use record `concept_id`
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