Update the age of onset pattern TSV

[rays22]

A simplified spreadsheet of the various combinations of clinical temporal measurement + diseases terms in the GWAS Catalog, and the suggested combined terms.

The spreadsheet includes the ID for each term and PMIDs of publications currently annotated with these combinations.

• [x] Work on updating the disease_onset.yaml (age of onset pattern) TSV on the OBA repo based on Elliot's gsheet

[rays22]

I am not sure what to take from Elliot's gsheet to update the disease_onset.tsv file. It has 22 MONDO disease terms. All of them are already in the disease_onset.tsv file. There are five more MONDO terms in in the disease_onset.tsv file compared with Eliot's table. Some of those terms have an equivalent non-MONDO term in Eliot's table:

disease	disease_label	DISEASE-TERM	DISEASE-TERM-ID
MONDO:0004985	psychotic symptoms, bipolar disorder	bipolar disorder	EFO:0000289
MONDO:0017276	Frontotemporal dementia	frontotemporal dementia	Orphanet:282
MONDO:0007739	Huntington disease	Huntington disease	Orphanet:399
MONDO:0001384	Myopia	myopia	HP:0000545
MONDO:0004892	refractive error	?	?
MONDO:0021661	coronary atherosclerosis	coronary atherosclerosis	EFO:0007938

In the DISEASE-TERM-ID column of Elliot's table there are

• 24 EFO terms,
• 3 HP terms,
• 3 Orphanet terms.

None of these terms are MONDO:0000001 disease or disorder terms as mandated by the disease onset pattern.

• [x] Discuss this issue at the meeting tomorrow.

[dosumis]

TODO

• [ ] Check EFO xrefs to find mappings to MONDO - If the terms are not already in the onset tsv, add them.
• [ ] Check Mondo for xrefs to Orphanet - If the terms are not already in the onset tsv, add them.
• [ ] Communicate back to EFO (Zoe) - potential EFO terms for obsoletion with replaced_by to MONDO

HP terms may need more discussion - add to agenda of monthly call.

[rays22]

If there were any classes missing from disease_onset.tsv than I need an explicit list of them together with appropriate MONDO:0000001 disease or disorder terms as mandated by the disease onset pattern. terms.