Stage Group: Map NAACCR to Cancer Modifier

[rtmill]

Given the version is stored in a separate field, the utility of this is unknown. That said, these values need to be de-standardized and may as well map them to the appropriate (albeit higher-level) concepts - i.e. without version included.

It will take a little extra work as the representation varies from typical numeric to roman numeral.

Target: stage_group_CancerModifier.csv

Source: stage_group_NAACCR.csv

[kzollove]

This table contains the destandardized NAACCR concepts: concept_NAACCRtoCM.xlsx This table contains the NAACCR concepts mapped to Cancer Modifier concepts: concept_relationship_NAACCRtoCM.xlsx

Snags/considerations:

1. There were three terms (occult, stage unknown, not applicable; one each for clin and path) in NAACCR that weren't represented in the stage_group_CancerModifier table.

   • Occult had a match in Athena, but it was not clin/path specific so I mapped both NAACCR terms to that one concept. I also destandardized in concept table
   • Stage unknown had no match that I could find, so I destandardized in concept table and did not map.
   • Not applicable was already non-standard. I did not include it in concept or concept_relationship table

2. We just leave standard_concept blank if non-standard, correct? This is what I did

3. Changing valid_end_date for the standard concepts. Do we need to include a row in the concept table where standard concept has valid_end_date updated?

ex: |concept_id|standard_concept|start |end | |1 | |8/15/2023|12/31/2099| |1 | S |1/1/1970 |8/15/2023 |

[kzollove]

concept_relationship_NAACCRtoCM.csv concept_NAACCRtoCM.csv