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monarch-initiative / omim

Data ingest pipeline for OMIM.
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"Included" symbols: Decide what to do #140

Open joeflack4 opened 2 months ago

joeflack4 commented 2 months ago

Background

Originally in #118 we were going to add these as synonyms. However, we realized that we are specifically not adding "included" titles and instead marking them as mondo#omim_included. We are currently thinking about what to do, and we may end up treating symbols in the same way.

Choices: a. oio:exactSynonym b. oio:relatedSynonym c. oio:closeSynonym d. mondo#omim_included

I think 'd' for now. If we choose to use a synonym type, then we should also do so for included titles as well. If we were to pick a synonynm type for these, I think would be 'related' or 'close'.

Related

joeflack4 commented 2 months ago

For now, as of this PR, I'm adding as mondo#omim_included:

twhetzel commented 2 months ago

Can you add some examples of what the original data looks like and what it does (or will) look like when it is processed?

joeflack4 commented 2 months ago

Sure. Maybe this is sufficient, but let me know if you're looking for a different kind of example:

OMIM:113600 a owl:Class ;
    rdfs:label "branchial cleft anomalies" ;
    MONDONS:omim_included "branchial cysts" ;
    oboInOwl:hasExactSynonym "branchial cleft anomalies" ;
    rdfs:comment "This term has one or more labels that end with ', INCLUDED'." .

This is an example of an existing class with MONDONS:omim_included on an included title.

Hypothetically, if this class also had an included symbol "BC", then it would look like this:

OMIM:113600 a owl:Class ;
    rdfs:label "branchial cleft anomalies" ;
    MONDONS:omim_included "branchial cysts" ;
    oboInOwl:hasExactSynonym "branchial cleft anomalies" ;
    MONDONS:omim_included "BC" ;
    rdfs:comment "This term has one or more labels that end with ', INCLUDED'." .