Open up for group discussion: Procedure relation hierarchies

[rtmill]

Problem Space

It is usually burdensome or impossible to query for procedures with specific context when creating a phenotype. Those include:

• site (site vocabulary varies by procedure vocabulary, or missing)
• type of procedure - e.g. resection, biopsy, destruction (variation of vocabularies, granularity, or missing)
• intent (not mapped and concepts can be ambiguous)

Proposed Solutions

Create standard hierarchies of concepts that can be used relationally to identify procedures based on context. These concepts would be leveraged similarly to how "site" and "histology" are related to ICDO3 concepts, i.e. "has site", "has histology" in the concept relationship table.

An aside, one of the difficulties that has slowed this down classifying procedures is the existence of data that contains 'high level' treatments, such as just the term "Chemotherapy", e.g. within tumor registries. This solution would have those concepts map to procedures (i.e. Chemotherapy, nos) but also have these same relational concepts (i.e. "has cancer procedure type: chemotherapy") associated with them.

Diagram from @mgurley showing a mock-up of a "Procedure type" hierarchy:

Additional questions from @mgurley

1. Can we build or steal? If so from where?
2. How many levels should be within the Treatment Hierarchy above existing procedure codes?
3. What domain? Procedure or something different?
4. Can we eliminate the Regimen domain and use Procedure for all?
5. Are we ok with cross-domain hierarchical relationships?

[rtmill]

Some example use cases:

Give me all the standard procedure concepts, across all vocabularies, that....

• are a "mastectomy"
• are a "biopsy"
• are a "destructive procedure" of the "breast"
• are "biopsy" procedures of the "breast"
• are "destructive procedures" for "any site within the trunk"
• are "diagnostic"
• are "any kind of excision" of a the "liver"
• are "excision" procedures of the "liver" with "diagnostic" intent