autism (disease) MONDO:0005260 missing MeSH ID

monarch-initiative / mondo

Mondo Disease Ontology

http://obofoundry.org/ontology/mondo

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autism (disease) MONDO:0005260 missing MeSH ID #1547

Closed lcdaugherty closed 4 years ago

lcdaugherty commented 4 years ago

autism (disease) (MONDO:0005260) Xref that should be fixed (MeSH: D001321)

Other comments: Just wondering why MeSH: D001321 is no longer included in this entry?

Thanks

nicolevasilevsky commented 4 years ago

Hi @lcdaugherty - I still see it listed as an xref, where are you looking?

lcdaugherty commented 4 years ago

Hi @nicolevasilevsky - I was looking here: https://monarchinitiative.org/disease/MONDO:0005260, am I looking at the wrong place?

nicolevasilevsky commented 4 years ago

@lcdaugherty - ah, I see! I'm not sure why it isn't showing up in Monarch.

@kshefchek can you help investigate? Thanks!

kshefchek commented 4 years ago

Monarch is currently running http://purl.obolibrary.org/obo/mondo/releases/2020-03-05/mondo.owl . I can close when we push our next data release (likely a few weeks out)

lcdaugherty commented 4 years ago

@nicolevasilevsky @kshefchek is this anything to do with absoluteMatch and closeMatch?

The MeSH ID for autism is not equivalent to the MONDO term -- in the OWL file OWL.edition of MONDO (v1.0), it's neither an equivalent class, nor an exact match.

https://monarchinitiative.org/disease/MONDO:0005260 only shows mappings that use the equivalence classes, not the cross references (as far as I can tell?)

OWL file states that the identifier is an exact match e.g. for autism:

BUT, the MeSH ID is denoted closeMatch not exactMatch MONDO:0005260 autism (disease) So, would the next release change the associated MeSH ID associated to autism (disease) MONDO:0005260 from closeMatch to exactMatch? Sorry for all these questions, as you can see I am getting a bit confused!

maglott commented 4 years ago

@kshefchek , @nicolevasilevsky A little off topic, but trying to reduce my confusion, too. I can tell frm https://www.ebi.ac.uk/ols/ontologies/mondo which release is being displayed.

where is the same information from Monarch?
what is the update cycle in Monarch for Mondo?

kshefchek commented 4 years ago

The monarch release cycle is dependent on a lot of factors, I would say at best monthly and at worst quarterly

kshefchek commented 4 years ago

where is the same information from Monarch?

@maglott I've added a ticket here for this to be added https://github.com/monarch-initiative/monarch-ui/issues/340

lcdaugherty commented 4 years ago

@nicolevasilevsky I might have a handful of similar cases to this, so would be good to know if the following is true or not?

So, would the next release change the associated MeSH ID D001321 associated to autism (disease) MONDO:0005260 from closeMatch to exactMatch?

nicolevasilevsky commented 4 years ago

@lcdaugherty apologies - I didn't realize this is what you were asking for - I made the MESH xref equiv to the Mondo term. This will be available in the next release in late July/early Aug

lcdaugherty commented 4 years ago

@nicolevasilevsky thank you for clarifying. I am returning to ontology related work after a few years not working with them, so it good to be able to make contributions again (where there is agreement of course!)