Best way to filter a list of diseases by those relating to the immune system?
1
0
Entering edit mode
4.4 years ago

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
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
4.4 years ago

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
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2058 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6