Incorporate feedback from manual reviews: HP/MONDO/MAxO matching

[tursynay]

From Pierrette in Slack data-harmonization-qc-team channel (December 4th, 2024):

Trish, for annotations of TEAM-DS and other studies, I propose the following - let me know if this makes sense

• If there's a close match in HP/MONDO/MAxO AND an "other" term listed, we keep only the HP/MONDO/MAxO terms to avoid redundancy.

  • E.g. "Wears glasses" has MAxO:0025004 (glasses usage) which seems redundant with the other annotated term SNOMED:225582009 (wears glasses), so I would delete the SNOMED term

• If there's no match in HP/MONDO/MAxO then we'll keep the other term, but still consider requesting a new term. I'll add a flag in the "Notes" column for term requests

  • e.g. "left handed" doesn't have an HP/MONDO term, so I would keep the SNOMED term, but consider making a new term request to HP?

• In that same row for "wears glasses" above, I just noticed that there are also annotations for "vision abnormality" in HPO/MONDO, which is not explicitly described in the source text. Is that inferred by harmonica, or is that something that you added manually Trish? In this case it's probably redundant and could be deleted since there's also a "visionpx" column with general annotations of "vision disorder". More generally, should we be adding annotations for conditions that aren't explicitly stated? (When I was doing everything manually, I usually only annotated the specific term for the sake of time.)