After refactoring the subclass of sync, a lot of changes

[matentzn]

Build PR for #8431

I eyeballed some of the, and they seem correct to me.. To review this:

1. Check out this file: https://raw.githubusercontent.com/monarch-initiative/mondo-ingest/main/src/ontology/reports/sync-subClassOf.confirmed.tsv (this is what is merged into mondo-edit)
2. Confirm that the changes reflect the changes you see to the edit file
3. Confirm that the changes to the sync-subClassOf.confirmed.tsv are intended

The most important is (3), as I already did 1 and a few spotchecks re 2.

I suggest @joeflack4 you take a look here is well.

[twhetzel]

I'm not sure I am looking at this in the "right" direction. For example, for MONDO:0000022 it has these changes:

- is_a: MONDO:0024290 {source="NCIT:C118172", source="icd11.foundation:1048673005"} ! enuresis
+ is_a: MONDO:0024290 {source="icd11.foundation:1048673005"} ! enuresis

So in Mondo MONDO:0000022 'nocturnal enuresis' is a subclassof MONDO:0024290 'enuresis'. The Mondo term has xref: icd11.foundation:1048673005 {source="MONDO:equivalentTo"} and icd11.foundation has this same subclassof relation between 'nocturnal enuresis' and 'enuresis' and is a source for subclassof relationship in Mondo. But the Mondo term also has xref: NCIT:C118172 {source="MONDO:equivalentTo"} and the subclassof relationship between between 'nocturnal enuresis' and 'enuresis' exists in NCIT, but NCIT:C118172 was removed as a source for the subclassof relationship in Mondo.

Also, many of the subclassof sources that were removed are from DOID and NCIT. When I looked in the mondo-ingest repo at tmp/component-download-ncit.owl.owl I could find 'nocturnal enuresis' and 'enuresis', but when I looked at components/ncit.owl I could not find either class 'nocturnal enuresis' and 'enuresis'.

[matentzn]

Also, many of the subclassof sources that were removed are from DOID and NCIT. When I looked in the mondo-ingest repo at tmp/component-download-ncit.owl.owl I could find 'nocturnal enuresis' and 'enuresis', but when I looked at components/ncit.owl I could not find either class 'nocturnal enuresis' and 'enuresis'

At first I found this concerning, but then I checked our specs and they clearly state that we only ever sync the neoplasm branch with NCIT. enuresis is in the psychiatric disorder branch..

The DO is more interesting/concerning:

[Term]
id: MONDO:0000248
name: dengue shock syndrome
xref: DOID:0050125 {source="MONDO:equivalentTo"}
is_a: MONDO:0005502 {source="DOID:0050125", source="MONDO:Redundant"} ! dengue disease

[Term]
id: MONDO:0005502
name: dengue disease
xref: DOID:12205 {source="MONDO:equivalentTo", source="EFO:0005547"}

And in DO:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_0050125">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_12205"/>
    <rdfs:label xml:lang="en">dengue shock syndrome</rdfs:label>
</owl:Class>

The confirmed subclass table is clearly missing this, only containing these two entries related to dengue:

MONDO:0005358	Dengue hemorrhagic fever	MONDO:0005502	DOID:12206	DOID:12205	dengue disease
MONDO:0000259	asymptomatic dengue	MONDO:0005502	DOID:0050143	DOID:12205	dengue disease

In my opinion its a bug in the subclass sync, one that we didn't notice because my previous subclass pipeline didn't delete all the evidence..

So, I think we need to:

• 1. File a bug report (if you agree it is one) (@twhetzel)
• 2. Fix that bug (@joeflack4)
• 3. Merge asap into main (maybe we should considering ditching the whole idea of a develop branch, its slowing us down a lot) (@twhetzel)
• 4. Make a new data release (@twhetzel)
• 5. Run the subclass pipeline Fix subclass of sync #8431 again (@matentzn)
• 6. Update this PR again (@matentzn)
• 7. Review again (@twhetzel)

let me know what you think

[twhetzel]

I added the ticket monarch-initiative/mondo-ingest#708, unclear what availability @joeflack4 has to fix this as an urgent priority. No, we're generally not ditching the develop branch. BUT in this specific case for the December release may need to make some careful adjustments to get these bug fixes addressed.

[twhetzel]

Converting to Draft until this is fixed monarch-initiative/mondo-ingest#708