[BiO BB] PUBMED --> Genes ??

Ann Loraine aloraine at gmail.com
Thu Nov 3 09:42:26 EST 2005


Is there anything that is scriptable?  E.g., I make a URL like:

http://someservice.org?gene=TP53

and read it like this:

import urllib
data = urllib.urlopen(url)
while 1:
  nicelyformattedline = fh.readline()
  ... and so on

Also, I think you can get Pubmed ids from Entrez Gene records, which
are downloadable from NCBI ftp site.

-Ann

On 11/3/05, Stefanie Lager <stefanielager at gmail.com> wrote:
> You can also try the iHOP service
> http://www.ihop-net.org/UniPub/iHOP/
>
>
> On 11/2/05, Dan Bolser <dmb at mrc-dunn.cam.ac.uk> wrote:
> > Hello,
> >
> > After playing with some stuff on the NCBI / PubMed site, I wonder if
> > there is a list mapping PUBMED ID to Gene ID (of some kind, like refseq
> > for example)?
> >
> > For a given gene I would like to look up all the associated literature.
> > Any recomendations on how to do that?
> >
> > Is there a tab delimited pubmed database that links pubmed id to
> > keywords for example?
> >
> > Cheers,
> > Dan.
> >
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--

Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu



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