generate report on alignment of Mondo with UMLS

[nicolevasilevsky]

A report is needed on what UMLS CUIs match to more than one Mondo term and vice versa? what is the provenance of those? Does any of the provenance come itself from multiple terms to one mondo or vice versa

cc @mellybelly

[nicolevasilevsky]

List of cases to find programmatically and review

• Gene-specific records with more than 1 exact XRef to OMIM
• labels that are both exact synonyms and related synonyms for the same record
• records that have multiple CUI from UMLS (i.e. C[0-9]+ pattern, not CN

[joeflack4]

I find the second comment you added w/ the 3 bulleted items more approachable than the original post, so I think I would start there if/when I start this.

Questions @nicolevasilevsky

1. What is a CUI?
2. Do you think the only file I would need to analyze for this report would be mondo.obo or mondo.owl?
3. I assume my work could be entirely done via SPARQL queries? Or do you have any other recommendation?
4. Where should I put the report script? src/scripts?

[nicolevasilevsky]

1. CUI = The Concept Unique Identifier for a Metathesaurus concept to which strings with the same meaning are linked. (See more info here)
2. Or you could search the mondo-edit.obo file
3. SPARQL sounds good
4. sure!

Thanks!

[joeflack4]

@nicolevasilevsky This is good, thanks. I think this is enough clarification for now. I probably still won't be able to get to this for a bit, but I now know where to start.

[nicolevasilevsky]

sounds good!