DO NOT MERGE: Bug: Synonym Sync: Duplicate rows - build

[joeflack4]

Build for:

• Bug: Synonym Sync: Duplicate rows #720

Best to check results in: the Google Sheet

Related:

• DO NOT MERGE: Bug: Synonym Sync: Duplicate rows - mini build #721

[joeflack4]

I'm sure this has nothing to do with this PR, and I'm sure this has been observed elsewhere, but I'm wondering why:

mondo-omim-genes.robot.tsv has only 20 lines changed, but mondo-omim-genes.robot.owl has over 30k.

[matentzn]

I mean, what is the diff? The most typical reason for huge diffs are genid s, so generated identifiers for anonymous expression necessary for RDF XML

[joeflack4]

@matentzn Ah, I see, you are correct. These are bnode identifiers.

     <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0013913">
-        <rdfs:subClassOf rdf:nodeID="genid5482"/>
+        <rdfs:subClassOf rdf:nodeID="genid5478"/>
     </owl:Class>
-    <owl:Restriction rdf:nodeID="genid5482">
+    <owl:Restriction rdf:nodeID="genid5478">
         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0004003"/>
         <owl:someValuesFrom rdf:resource="http://identifiers.org/hgnc/11528"/>
     </owl:Restriction>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0013913"/>
         <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
-        <owl:annotatedTarget rdf:nodeID="genid5482"/>
+        <owl:annotatedTarget rdf:nodeID="genid5478"/>
         <oboInOwl:source>OMIM:614840</oboInOwl:source>
     </owl:Axiom>

Not the hugest problem, but would make reviews easier if these IDs were deterministic. I have some Python code to do that in the OMIM pipeline, but that wouldn't be helpful here. Not that we have to worry about it now, but do you think there's a way?

[matentzn]

Yes, switch to functional syntax in ROBOT! convert -f ofn

[joeflack4]

Ah, I see. But not in RDF/XML.
I have begun to take a great liking for OFN now not because of its syntax, but because of its determinism in general, and the ease of diffing it, for that reason as well as fewer lines. This is now a regular part of some of my workflows.

[joeflack4]

@twhetzel This file has nothing to do with this PR. But any idea why this has so many new rows?

Note that the other OMIM unmapped files do not have such a large diff:

docs/reports/unmapped_omim.md                      |      6 +
.../lexmatch/mondo-only/unmapped_omim_mondo.tsv    |      7 +-
src/ontology/lexmatch/unmapped_omim_lex.tsv        |      2 + 
src/ontology/reports/omim_unmapped_terms.tsv       |      6 +
rc/ontology/unmapped/omim-unmapped.owl             |  45170 +++++-

[joeflack4]

General review

Other than some OMIM related oddities not related to this PR, LGTM!