Discuss, evaluate and implement approach for NAACCR hierarchies and new standard concepts vs existing

[sratwani]

Discuss proposal/approach to
(1) Create new standard concept vs choose one of the existing concepts

organ@4121@1 -Maps to -4121@1 (new concept)
organ@4121@1 -Is a -4121@1
organ1@4121@1 -Maps to -organ2@4121@1 (chose organ2-code as a standard one)

(2) Built hierarchies in NAACCR
If one answer is metastatic cancer and the other is metastases to the bone, link metastatic cancer -> metastases to the bone in a hierarchy

[sratwani]

@dimshitc -> This is the discussion that Rimma was referring to for the CAP solution as well.

(1) For duplicate entries between diff schemas when they mean the same (same semantic concept) but repeat for each diagnostic schema, the question is, should we pick and choose 1 and map all others to this one and make it non standards OR create a new concept make it standard and add all the existing concepts to this standard.
(2) For entries where there are similar but diff degree of granularity. In preparation for mapping to standards, we need to identify which is more granular and less granular and put them in a hierarchy accordingly.
For (1) above (example questions is ‘which organ did the tumor metastasis’), the recommendation is to create a new one instead of arbitrarily using one of the existing one. Reason for this is as we know we are ultimately going to replace this by either SNOMED or LOINC based on consensus building with Campbell Brothers and possibly others. So, this is like a place holder for the future consented standard concept. This approach will also mean no change to the ETL. We will create a new one which will be easy to replace. Assign vocabulary_id to ‘NAACCR extension’ and concept_code to ‘OMOP_surrogate’ (OMOP followed by some random number).
There is a follow-up to discuss with Parsa. We don’t have vocabulary for relationship, we need to discuss this with Parsa.
For (2) above (example question is ‘did the tumor metastasis’), do we want to do anything to connect the 2 observations (‘which organ did the tumor metastasis’ and ‘did the tumor metastasis’). Rimma has sent the list of pairs to Dima. Plan is to take a look at these offline and understand the scope of the problem. Follow-up in the next Vocabulary call as this might affect the ETL.

[sratwani]

@dimshitc Can this issues be closed. I believe the Cancer Modifier vocabulary makes this issue obsolete?