Gene Or Protein Queries In Pubmed

Question

[miquelduranfrigola]

Hi all,

I have a list of proteins that I have found associated with several MeSH disease terms. This is a rather long list of protein-disease pairs, right now as (UniProt AC; MeSH ID). I'd like to have an idea of what proportion of these pairs co-occur in PubMed abstracts and titles.

Diseases are not an issue because I already have the MeSH term, which I can query directly in PubMed. But how about the proteins? How would you guys approach this programmatically?

Thanks!

PS: I'd also like to be able to do this with (GO ID; MeSH ID) and (KEGG ID, MeSH ID) pairs... But this will require a new post, I'm afraid...

Answer 1

[Pierre Lindenbaum]

I would use the NCBI elink API. For example, to find the pubmed articles for gene id 10364289 ( http://www.ncbi.nlm.nih.gov/gene/10364289 )

the URL is: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&dbto=pubmedcmd=neighbor&retmode=xml&id=10364289

it returns the following paper: http://www.ncbi.nlm.nih.gov/pubmed/21725009