Hi All !
Can anyone tell me about a text mining (pubmed) tool that looks for GWAS data like SNPs RS Ids, considering some information like the population studied, their size, the trait ...
Thank you
Radhouane
This is not a direct answer to your question, but you might not be aware of these two resources that have tried to answer your question and questions like it:
I know that there is a team of people at NHGRI that manually goes through the GWAS papers to extract the data entered into that catalog. A text parser will miss information, especially if it is in a supplemental file. Abstracts are often incomplete in terms of which allele increases risk and sometimes even the exact SNP(s) involved in the association.
Maybe MarkerInfoFinder or HuGE Navigator will do what you are looking for.
It might be useful to look at the GWAS Integrator for your project. This is introduced in a recent paper entitled GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies. Some of these authors brought us HUGE Navigator.
GRAIL is the GWAS + text mining tool that you'll want to try, and seems to get more to the point of the question as posed. GRAIL (Gene Relationships Across Implicated Loci) essentially takes a list of SNPs and maps those SNPs to gene regions using linkage disequilibrium. Then, the tool uses a simple text-mining algorithm to draw connections among the associated genes.
See here what Mary wrote about GRAIL two years ago this week. Another fine overview of GRAIL is here.
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