I heard about a tool which lets you search for papers based on a set of genes that you input and it returns papers that have mentioned a significant set of those genes.
Does anyone know what tool this is?
related of Linking Genes/Diseases To Pubmed Ids
In R you can do this using Org.HS. Below is an example:
# mapped_genes are all the genes that org.HS.egPMID covers (the HS refers to homosapien). These genes are in Entrez format.
# entrez2Pmid is a list taking entrez gene ids to a vector of Pmids.
mapped_genes <- mappedkeys(org.Hs.egPMID)
entrez2Pmid <- as.list(org.Hs.egPMID[mapped_genes])
# now if you have an entrez gene id you can look up the relevant papers by doing
(here is a pastebin of the code since I stink at using the biostars code formatter http://pastebin.com/JCa6L7sB)
There is a tutorial here:
Also you can just use http://idconverter.bioinfo.cnio.es/IDconverter.php. Although I've found that sometimes the results seem to be a subset of the results you get using the method outlined above.
Also I haven't used it much but chilibot (does anybody know of a more updated approach?) does some NLP on papers mentioning genes in a gene set to build a biological network.
The software is called GeneValorization and is available as a Java Web Start application.
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