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Change CIViC classification to match ClinVar enum #452

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korikuzma opened this issue Feb 27, 2025 · 1 comment · Fixed by #455
Closed

Change CIViC classification to match ClinVar enum #452

korikuzma opened this issue Feb 27, 2025 · 1 comment · Fixed by #455
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korikuzma commented Feb 27, 2025 •
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Feature description

@larrybabb suggested that the CIViC transformer should use the ClinVar clinicalImpactClassificationDescription enum: https://github.com/ncbi/clinvar/blob/master/submission_api_schema/submission_api_schema.json#L510-L514

Use case

Since we're submitting the CIViC assertions generated by the MetaKB Transformers, we should be consistent with the values we're using. Since ClinVar already defines an enum, we should follow this.

Proposed solution

Tier I -> Tier I - Strong
Tier II -> Tier II - Potential
Tier III -> Tier III - Unknown
Tier IV - Benign/Likely benign

Alternatives considered

No response

Implementation details

No response

Potential Impact

No response

Additional context

No response

Contribution

Yes, I can create a PR for this feature.
@korikuzma korikuzma added the enhancement New feature or request label Feb 27, 2025
@korikuzma korikuzma self-assigned this Feb 27, 2025
korikuzma added a commit that referenced this issue Feb 27, 2025
@korikuzma
feat!: change civic classification.primaryCode to use clinvar enum
1216596 
close #452

* Use ClinVar Submission `clinicalImpactClassificationDescription` enum
@korikuzma korikuzma mentioned this issue Feb 27, 2025
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@korikuzma korikuzma linked a pull request Mar 4, 2025 that will close this issue
feat!: change civic classification.primaryCode to use clinvar enum #455
Merged
korikuzma added a commit that referenced this issue Mar 7, 2025
@korikuzma
feat!: change civic classification.primaryCode to use clinvar enum (#…
add4368 
…455)

close #452

* Use ClinVar Submission `clinicalImpactClassificationDescription` enum
@github-actions github-actions bot closed this as completed Mar 7, 2025
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github-actions bot commented Mar 7, 2025

Closed by #455.

korikuzma added a commit that referenced this issue Mar 9, 2025
@korikuzma
feat!: change civic classification.primaryCode to use clinvar enum (#…
4e435d2 
…455)

close #452

* Use ClinVar Submission `clinicalImpactClassificationDescription` enum
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feat!: change civic classification.primaryCode to use clinvar enum cancervariants/metakb
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