network USA

[Peter Rice]

David Mathog wrote:
> 
> Today I finally realized that the NCBi's PmFetch cgi
> 
>   http://www.ncbi.nlm.nih.gov:80/entrez/utils/pmfetch_help.html
> 
> can be used to retrieve data via gi using a "simple" URL like this:
> 
> wget -O dmwhite.genbank \
> 'http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi?db=Nucleotide&id=10873&report=gen&mode=text'
> 
> Unfortunately it seems not to be able to retrieve by either accession
> number or
> locus name - I'm still waiting to hear if there is some other NCBI
> interface for that.

Oops. Will be fixed in 2.4.0 (Alan and I thought it already was, but it
needed one extra line of code in the latest CVS version). The problem is
that EMBOSS checks the ID and accession of the returned entry for the URL
access method, and of course neither matches '10873'.

Which leads on to a new access method for 2.4.0. We are adding an "srswww"
access method that generates the SRS URLs, and can query by id, accession,
seqversion (or GI), keyword, organism or description. We can add at least
some of these for entrez (new access method entrez) if we can gather up
enough URLs. Are there any entrez experts who can help with suggested URLs
to retrieve (preferably plain text, but html will do) from entrez with
queries for each of these fields?

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723