Precaution: Don't add mappings/refs for deprecated/removed MIMs

[joeflack4]

Overview

If a MIM has been deprecated or removed, I do not know if this will result in any changes to the data coming in through the API. My guess is that it will show that the MIM had been updated, and we will fetch data for that MIM. But my guess is also that if they delete/deprecate a MIM, they may still leave any PMID refs and mappings in their database.

The result is that, if this happens, we could end up adding PMID mappings and references for MIMs that have been deprecated or deleted.

Solution

If we want to be cautious, then we could use this variable which I believe shows only active (might still include deprecated?): omim_ids:

omim/omim2obo/main.py

Line 208 in c67c68f

omim_ids = list(omim_type_and_titles.keys())

And then add a line above here: if row['mim'] in omim_ids:

omim/omim2obo/main.py

Line 434 in c67c68f

graph.add((OMIM[str(row['mim'])], pred, obj_ns[_id])) # IAO:0000142: 'mentions'