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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Emma ingest question #929

Closed matentzn closed 3 years ago

matentzn commented 4 years ago

Just listened to a talk where someone was mentioning the EMMA resource/

https://www.infrafrontier.eu/emma-strains-and-rare-diseases

Are these (the variant->disease annotations) imported through the MGI pipeline (I can see lots of EMMA terms in @TomConlin s curie counts)?

TomConlin commented 4 years ago

7.2k EMMA appear in the Dipper MGI ingest as owl:sameAs to some MGI

noticeable in: https://archive.monarchinitiative.org/latest/visual_reduction/release/mgi.gv determining if those MGI the EMMA are the same as are; variants associated with a disease would take a second deeper look.

Would you like me to do that?

matentzn commented 4 years ago

Thanks for checking! Not sure you have to spent time on it; Lets keep it in mind for after the renewal perhaps?

TomConlin commented 4 years ago

maybe jot down your thoughts , I have just spent a bunch of time in MGI's database looking to make how we fetch from them more robust so the timing now is better than average.

matentzn commented 4 years ago

It was really just that I was listening to a rare disease talk in the context of the European Joint Programme of Rare Diseases, and they mentioned that they wanted to integrate with resources such as that one.

kshefchek commented 4 years ago

solr is also great for queries like these, but I wasn't able to turn anything up in any association that we index.http://www.informatics.jax.org/strain/MGI:2655911 has the most edges connected to it, but looks like mostly GENO model construction.

matentzn commented 4 years ago

Maybe if this source (EMMA) turns out interesting, we can consider making it a primary ingest after renewal approval.