Health-Informatics-UoN / Carrot-Mapper

Carrot: Convenient And Reusable Rapid Omop Transformer.
https://carrot4omop.ac.uk
MIT License
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Mapping reuse feature forcing the automated mapping to map to incorrect concept_id #778

Open erummas opened 3 days ago

erummas commented 3 days ago

Is there an existing issue for this?

Current Behavior

I am observing that mapper is generating incorrect automated mappings (V) OPCS4 codes that have reused concepts from previous scan report(s) For example: OPCS4 code Z50.2 should map to concept_id 4144227 Standard SNOMED ; This concept_id is pulled via reuse feature from another scan report with the correct concept_id but at the same time an automated concept_id is generated 44516478 Non-Standard OPCS4 concept. _This shouldn't be happening because automated mapping should always map to standard conceptid. Also I was of an impression that Anatomic Site is not implemented yet. The code Z50.2 is from domain Spec Anatomic Site so I am assuming this has been implemented now?

More cases can be seen in screenshot or here -> https://carrot.ac.uk/scanreports/645/tables/3656/fields/141306/ https://carrot.ac.uk/scanreports/645/tables/3656/fields/141306/ I have checked ICD10 codes too but it seems only OPCS4 codes are affected by this bug.

mapper-5

Expected Behavior

Map OPCS4 codes to standard concept_id

Steps To Reproduce

More cases can be seen in screenshot or here -> https://carrot.ac.uk/scanreports/645/tables/3656/fields/141306/

Environment

- OS:
- Other environment details:

I'm part of a Project Team

No response

Anything else?

No response

Are you willing to contribute to resolve this issue?

None