[Bioperl-l] Downloading UID Lists

Francis Ouellette Francis Ouellette <francis@cmmt.ubc.ca>
Sun, 11 Feb 2001 23:20:41 -0800 (PST)

Dear David,

not really a bioperl question, but you need to add "&dispmax=some_mumber" 
where "some_number" is the number of hits you want back. 

I should warn you that this kind of use of the NCBI server is quite
excessive, and you should try other venues, like batch entrez, where
it's easy to get all 80 or 100,000 uids (gi numbers) with minimal
impact (batch entrez sets up a simple ftp session with all of the
data transfred at once). Unfortunatly, the batch entrez documentation
doesn't tell you how to write URLs to get this, but I'm sure
info@ncbi.nlm.nih.gov (or Sergei Shavirin, the Batch Entrez
creator, maintainer and talented author) would be happy to help you.

batch entrez is found at:


(but like I said, not really a bioperl question :-)



| B.F. Francis Ouellette                      Tel: (604) 875-3815 | 
| Director, Bioinformatics Core Facility      Fax: (425) 740-6978 | 
| CMMT, UBC, Canada                        http://www.cmmt.ubc.ca | 
| francis@cmmt.ubc.ca                http://www.bioinformatics.ca |

 On Mon, 12 Feb 2001, David Schibeci wrote:

> Date: Mon, 12 Feb 2001 14:36:39 +0800 (WST)
> From: David Schibeci <schibeci@arginine.murdoch.edu.au>
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Downloading UID Lists
> Hi,
> I'm trying to write a perl program which downloads a list of UIDs for a
> given legume (Medicago Truncatula) and then check against a list of
> previously downloaded sequences (via Network Entrez) and download any new
> sequences.
> I've gotten most of it to work (downloading sequences and checking against
> previously downloaded sequences) but I can't work out how to get a list of
> UIDs via the web (I can via Network Entrez, but I want to automate the
> entire process). I've tried using the search URL
> (eg.
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=Medicago%20%Truncatula[ORGN])
> but it limits me to twenty UIDs. I want to get all 80,000+.
> Can anyone help?
> Cheers,
> David
> ------------------------------------------------------------------------------
> David Schibeci
> Professional Officer
> Centre for Bioinformatics and Biological Computing
> Murdoch University
> South Street
> Murdoch WA 6150
> Phone: 61 8 9360 2790
> E-Mail: schibeci@cbbc.murdoch.edu.au
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