[Bioperl-l] Perl script to extract from ncbi

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Fri Feb 9 09:20:10 EST 2007


This is an example for fetching two GenBank records
(id=124504630,110665734) in XML format. Organism names like
'<GBSeq_organism>Rattus norvegicus</GBSeq_organism>' can be parsed from
the XML. 

 

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i
d=124504630,110665734&retmode=xml&rettype=gb

 

 

Or you can get TaxIds and translate them into real names:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nucleotide
&id=124504630,110665734&retmode=xml

 

Wenwu Cui, PhD

 

-----Original Message-----
From: George Heller [mailto:george.heller at yahoo.com] 
Sent: Thursday, February 08, 2007 1:55 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Perl script to extract from ncbi

 

Hi all, 

   

  I have a question regarding extracting data from Ncbi. I have a
database to store the sequence data, but the files I have loaded into
it, dont have a proper description line specified. Based on the
accession number, I need to find out what is the genus and species name
() from ncbi. 

   

  I have about 1500 records for which I need to extract the names from
ncbi. 

   

  Any ideas of how I can go about writing a perl script for extracting
this information from ncbi?

   

  Thanks!

  George.

 

 

---------------------------------

Now that's room service! Choose from over 150,000 hotels 

in 45,000 destinations on Yahoo! Travel to find your fit.

_______________________________________________

Bioperl-l mailing list

Bioperl-l at lists.open-bio.org

http://lists.open-bio.org/mailman/listinfo/bioperl-l




More information about the Bioperl-l mailing list