What information about VARIANTS are found in biomedical literature rather than diseases?
Entering edit mode
6.8 years ago

I am building a text mining application to extract information on variants found in biomedical literature. I thought of finding all the information mentioned about variants in literature at first. But now I think its quite impossible. 

If I can specifically say i'm finding this information about variants, it will be quite feasible. Already there are systems capable of finding variant-disease relationship, variant-gene relationship. So other than those, what are the other commonly found information about variants in biomedical literature? (My source will be PubMed). Or what latest tedetails about variants can I say i'm going to consider? 

P.S - I need this for my undergraduate project. Please help!

text mining variants mutations publications pubmed • 1.6k views
Entering edit mode
5.1 years ago

Perhaps The European Variation Archive (EVA), the EMBL-EBI’s open-access genetic variation archive could be helpful as a resource. They do link to publications for the studies were a variant was mentioned

Entering edit mode
4.4 years ago
Denise CS ★ 5.2k

You could also get the allele frequencies for genetic variants. Alleles that are rather common are unlikely to have a role in disease, unless it confers some sort of selection (classic example is the variant in HBB in people leaving in regions endemic for malaria). Another piece of information that you could get is on odd ratio from GWAS papers, clinical significance, etc.

With LINK, the latest Open Targets tool, you can find other connections (than diseases and phenotypes) from PubMed abstracts e.g. connections with drugs. Let's suppose you are interested in rs3862434 for example. More on LINK head to the Get to know LINK and explore 500+ million relations from PubMed abstracts post.


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