Many synonyms in Mondo are lacking up to date provenance

linikujp commented 7 months ago

Mondo term (ID Label) MONDO_0015541 (hereditary hemophagocytic lymphohistiocytosis) and many other terms

Bug/Typo/Error description The exact synonyms that are supposed to be Orpha:158038 (primary hemophagocytic lymphohistiocytosis) and Orpha:504 (familial hemophagocytic lymphohistiocytosis). However, the axioms of Orpha:504 shows MONDO:cjm .

<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0015541"/>
    <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
    <owl:annotatedTarget>primary hemophagocytic lymphohistiocytosis</owl:annotatedTarget>
    <oboInOwl:hasDbXref>Orphanet:158038</oboInOwl:hasDbXref>
</owl:Axiom>

<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0015541"/>
    <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
    <owl:annotatedTarget>familial hemophagocytic lymphohistiocytosis</owl:annotatedTarget>
    <oboInOwl:hasDbXref>MONDO:cjm</oboInOwl:hasDbXref>
</owl:Axiom>

The MONDO:cjm shows in many places in the MONDO file, not sure if it is an error or anything else.

See obo-community Slack workspace, the MONDO-community channel, the post by Asiyah Lin on March 19, 2024. and the replies from community members.

Your nano-attribution (ORCID) 0000-0003-2620-0345

matentzn commented 7 months ago

@linikujp thank you for the report.

MONDO:cjm is a provenance statement that means: Chris J. Mungall has reviewed this synonym manually and confirmed it. @nicolevasilevsky has removed MONDO:cjm in favour of his ORCID now.
There can be multiple provenance statements for the same synonym, including multiple ontology terms, and multiple human reviewers.
In your example, http://purl.obolibrary.org/obo/MONDO_0015541 is simply missing the Orpha:504 reference, which could be because we have not synced up our synonym source https://github.com/monarch-initiative/mondo-ingest/issues/88 for a while.

@twhetzel @sabrinatoro I renamed the issue now - the remaining issue here to discuss is purely when we will be able to prioritise our synonym sync.

twhetzel commented 7 months ago

I believe Orpha:504 in the original post should be Orpha:540.

twhetzel commented 2 months ago

The first phase of updating synonym provenance for "confirmed" synonyms (those that match the synonym label and scope) between Mondo and the source is aimed to be added into Mondo for the October release.

linikujp commented 2 months ago

@twhetzel what are the technical details (e.g. another annotation axiom?) to implement the "confirmed" provenance of synonyms? Is there any document to share? I also reported two bugs related to ExactSyn https://github.com/monarch-initiative/mondo/issues/8089 https://github.com/monarch-initiative/mondo/issues/8085

monarch-initiative / mondo

Many synonyms in Mondo are lacking up to date provenance #7465