A few synonym representation issues based on the review of the synonym sync "added" PR

[twhetzel]

Based on this PR review for this commit diff, there were a handful of very minor items related to representation of synonyms from OMIM. This ticket lists these issues to document them.

(1) there are a handful of synonyms from OMIM in the diff that still have "..., formerly" EXACT
Examples:
synonym: "ANOP1, formerly" EXACT [OMIM:301590]

synonym: "maa" RELATED [OMIM:309800]`
+ synonym: "MAA, formerly" EXACT ABBREVIATION [OMIM:309800]

+ synonym: "microphthalmia, syndromic 4" RELATED [OMIM:309800]
synonym: "microphthalmia, syndromic 4, formerly" EXACT [MONDO:Lexical, OMIM:301590]

synonym: "deafness, autosomal recessive 105" NARROW [OMIM:616958]
- synonym: "deafness, autosomal recessive 105, formerly" EXACT [OMIM:608653]

synonym: "intellectual developmental disorder with gastrointestinal difficulties and high pain threshold" EXACT [OMIM:617450]
- synonym: "intellectual developmental disorder with gastrointestinal difficulties and high pain threshold, formerly" EXACT [OMIM:617450]

synonym: "neurodevelopmental disorder with brain, liver, and lung abnormalities" EXACT [OMIM:618007]
- synonym: "neurodevelopmental disorder with brain, liver, and lung abnormalities, formerly" EXACT [OMIM:613658]

synonym: "cap myopathy 1" EXACT []
- synonym: "cap myopathy 1, formerly" EXACT [OMIM:255310]

(2) synonym: "ERYTHROCYTE ADA, ELEVATED, HEMOLYTIC ANEMIA DUE TO" EXACT ABBREVIATION [OMIM:301083] --> this is not an abbreviation

(3) synonym not parsed correctly. The OMIM content is not being parsed correctly for https://omim.org/entry/609029 so the value 22) is incorrectly represented as a synonym in omim.owl.

These are all very minor issues and may be an issue with the omim data files and/or an issue already resolved.

[joeflack4]

(2) this is not an abbreviation

This is due to a mistake where there is a missing ;; delimiter after "HAEADA" in the string "ADENOSINE DEAMINASE, ELEVATED, HEMOLYTIC ANEMIA DUE TO; HAEADA; ERYTHROCYTE ADA, ELEVATED, HEMOLYTIC ANEMIA DUE TO". An email was sent to the OMIM team entitled "301083 alt title;symbol syntax mistake". Our current plan is to wait for them to address the issue, and when they resolve it, the update will come through in the sync.

[joeflack4]

(3) synonym not parsed correctly

This is a bug in the OMIM ingest. We should be splitting on ; , with a space after it, not just ;. I will make a PR:

• Bug fix: title symbol splitting #193

[joeflack4]

(1) Synonyms that still have ", formerly"

I'm not actually seeing this in omim.owl, or in any of the OMIM synonym sync outputs. This should go away the next time that we run a synonym sync.

You can see by looking at this file from one of our recent builds: https://github.com/monarch-initiative/mondo-ingest/blob/fix-ordo-mapping-data2/src/ontology/reports/sync-synonym/synonym_sync_combined_cases.robot.tsv

There are some synonyms with "formerly". They are all DOID or NCIT, but none OMIM.

[joeflack4]

(4) Synonyms that are marked exact when they should be related

@twhetzel For a lot of the examples in (1), you also mentioned in the comment in #8584 that they were showing up as exact when they should be related. But I ran the synonym sync and they are all showing up in related. Let me know if you want me to post examples.

[twhetzel]

For (4) - that's fine, that is just how they showed up in the diff mentioned in the original comment in this issue.