Make FNCLCC grading concepts standard again

[rtmill]

While there are only 3 codes, they are currently duplicated so there are 6 concepts to change.

Suggestion: Choose a set of three and standardize, map the other 3 to the new standards.

Concepts: grade_fnclcc_concepts.xlsx

[kzollove]

3 concepts are set to standard in the concept table and the other 3 are unchanged.

In the concept_relationship table, the 3 newly standard concepts are mapped to/from themselves. The 3 non-standard are also mapped to/from the new standard concepts. Finally, the 3 new standard concepts are represented as children of the generic Cancer modifier Grade concepts for example Grade 1 Tumor.

[kzollove]

The only snag is if/when/how to change (remove) existing concept_relationship entries. For example, all FNCLCC concepts are currently "replaced by" and "mapped to" the more generic Cancer Modifier grade concepts:

For the 3 new standard concepts, I propose that these relationships are both removed and replaced with an Is a/subsumes relationship (as mentioned above)

For the 3 FNCLCC non standard concepts that map to the 3 new standard concepts, I propose that these relationships are both removed and replaced with the single Maps to/From relationship with the 3 new standard concepts.

The harder part is how to represent (and execute) removing existing concept relationships using the simple concept/concept_relationship representation of vocabulary changes?

[kzollove]

Use invalid_reason = 'D' to represent deleted concept relationships

From CDM conventions 5.4 spec:

Reason the relationship was invalidated. Possible values are ‘D’ (deleted), ‘U’ (updated) or NULL.

[cgreich]

The harder part is how to represent (and execute) removing existing concept relationships using the simple concept/concept_relationship representation of vocabulary changes?

You don't. Go through the Community Contribution process. Making concepts standard is not yet there in self-service. Contact the Vocab Team.

[rtmill]

The harder part is how to represent (and execute) removing existing concept relationships using the simple concept/concept_relationship representation of vocabulary changes?

You don't. Go through the Community Contribution process. Making concepts standard is not yet there in self-service. Contact the Vocab Team.

@cgreich This is regarding the development sprint where we will be building and persisting a delta of the vocabularies to facilitate short-term adoption (and eventually be folded back into the standard vocabularies).

[kzollove]

Along with plan outlined above, all existing relationships are marked with invalid reason "D" in concept_relationship table

concept_FNCLCC.csv concept_relationship_FNCLCC.csv