Exclude `Orphanet:377788` from rare subset pipeline

[joeflack4]

Overview

Exclude Orphanet:377788 "Disease" from the rare disease subset generation pipeline.

Context

See this discussion thread:

• https://github.com/monarch-initiative/mondo-ingest/pull/510#discussion_r1592954704

Nico:

Please exclude MONDO:0000001	http://purl.obolibrary.org/obo/mondo#ordo_disease	Orphanet:377788	disease	disease

From the ORDO subset - which is the "ORDO" disorder class itself. Adding this makes the entire ontology become "rare"!

Joe:

Orphanet:377788 "Disease" is a direct subclass of Orphanet:557493 "Disorder", which is one of the subsets that we've selected.

Nico:

I didn't realise "disease" was a subclass of "disorder"... create an issue to... exclude the term from the rare disease subset generation pipeline (with the logic that, while the term is, indeed in the ordo_disorder subset, it should not be added to the rare disease subset, which you are not concerned with here).

[matentzn]

To be clear, Orphanet:377788 is already excluded from the rare disease subset - this issue is about explicitly excluding it from the rare subset pipeline. Thanks @joeflack4, will take care of it!

[joeflack4]

Thanks for clarification! I'm completely in the dark on this side of things; those two things sound almost identical. I updated the title~

[matentzn]

This commit fixes it, and the PR around it will eventually close this issue, when it is merged: https://github.com/monarch-initiative/mondo/commit/4e98177428ee9ea5f4b4f5945c643e951a34edbc