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OHDSI / OncologyWG

Oncology Working Group Repository
https://ohdsi.github.io/OncologyWG
Apache License 2.0
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Top-level concept required for all clinical stage and all pathological stage concepts #641

Open gkennos opened 6 months ago

gkennos commented 6 months ago

To support the use case of querying condition occurrences that have pathological confirmation only, we need to insert in the staging hierarchy a top-level 'AJCC/UICC pathological stage' and 'AJCC/UICC clinical stage' term.

csv attached has proposed list for existing concepts that would be direct children of these new concepts

needs_parent.csv

cgreich commented 6 months ago

@gkennos: If you are looking to realize a "pathologically confirmed XYZ" this would work if the path lab provided a TNM report. If it didn't, or it didn't get recorded, or it is not applicable (like for hematological conditions), you would not catch that.

I would look for a condition_type_concept_id=32835.

Still wouldn't hurt to have your hierarchical concepts.

gkennos commented 6 months ago

Sure, but these aren't from path reports. They are recorded diagnoses with explicit stage, and a stage-type flag to select either clinical or pathological, so the valid type concept is 32840

cgreich commented 6 months ago

Not following. Pathologically confirmed diagnoses are not from path labs? Where else?

An EHR problem list is something that the patient declares to the provider. Has nothing to do with cancer diagnoses.

And again, no problem with those hierarchical concepts.

rtmill commented 6 months ago

Thanks @gkennos for putting together that list. This is definitely an upgrade and something we missed on our upcoming proposal about refining the hierarchies of tumor findings, specifically around staging & grading. Adding this to that ticket.

rtmill commented 6 months ago

Folded into the overall stage/grade hierarchy improvement discussion here: https://github.com/OHDSI/OncologyWG/issues/558#issuecomment-2000164032