Question

Best way to filter a list of diseases by those relating to the immune system?

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4.5 years ago

psyc_biostars ▴ 20

I have a list of diseases which I got from GWAS Catalog associations. However, I want to be able to filter these out systematically (via R), leaving only diseases related to the immune system.

Does anyone have any suggestions for how to do this? I thought it might be an idea to get a list of all immune diseases and all immune cell types, and to keep any entry that mentions those terms.

R • 1.0k views

ADD COMMENT • link updated 4.5 years ago by Pierre Lindenbaum 164k • written 4.5 years ago by psyc_biostars ▴ 20

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Please add more relevant tags. Is R really the only relevant tag here?

ADD REPLY • link 4.5 years ago by Ram 44k

score 2 · Answer 1 · 2020-06-03

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4.5 years ago

Pierre Lindenbaum 164k

GWAS use the Experimental Factor Ontology https://www.ebi.ac.uk/ols/ontologies/efo . There is an associated OWL file for download . I've got a tool that performs a very basic scan over all the simple children of a given term. For immune system disease I get the following terms that you can use to 'grep' the database.

ADD COMMENT • link 4.5 years ago by Pierre Lindenbaum 164k

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Great resource, thank you - what is the tool that you use to do this?

ADD REPLY • link 4.5 years ago by psyc_biostars ▴ 20

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https://github.com/lindenb/jsandbox/blob/master/src/sandbox/tools/owl/OWLTool.java

ADD REPLY • link 4.5 years ago by Pierre Lindenbaum 164k