[Bioperl-l] RE: [Pubmednew] Problem with esearch.fcgi

[Holland, Richard]

Hi,

Thanks for your answer regarding non-accessible accessions via
esearch.fcgi, but it doesn't quite solve my problem.

I am accessing GenBank programmatically via a set of modules called
BioPerl (http://www.bioperl.org/), specifically Bio::DB::GenBank. These
access the database on my behalf via the esearch.fcgi script. They
depend on the script returning the plain GenBank file without any HTML
markup.

The URL you sent me in response to my original question marks up the
response in HTML, and doesn't return just the plain GenBank file on its
own. 

My question was why are the two scripts unable to agree on the existence
of a particular accession (XM_055766)? Surely they are accessing the
same database under the hood? Are there any plans to make esearch.fcgi
recognise these more recent accessions?

I am copying this email to the BioPerl mailing list in case somebody
there can help out too.

BioPerl people - what are the alternatives? I am having the same
problems with the EBI servers, dbfetch, and Bio::DB::EMBL, which also
does not believe that the accession XM_055766 exists (although I can see
it quite clearly using Entrez at the NCBI).

cheers,
Richard

---
Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279



-----Original Message-----
From: Monica Romiti [mailto:romiti at ncbi.nlm.nih.gov] 
Sent: Tuesday, 7 October 2003 1:42 p.m.
To: Holland, Richard
Cc: romiti at ncbi.nlm.nih.gov
Subject: FW: [Pubmednew] Problem with esearch.fcgi


Dear Colleague,

Use:


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&t
erm=XM_0
55766[accn]&doptcmdl=GenBank


Best regards,

Monica at NCBI
-----Original Message-----

From:  custhelp at mail.nlm.nih.gov
Sent:  10/4/2003 04:24:45 PM
To:  Richard.Holland at agresearch.co.nz
Subject:  [Pubmednew] Problem with esearch.fcgi

Richard Holland:

Your email has been forwarded to the National Center for Biotechnology 
Information (info at ncbi.nlm.nih.gov)

Ellen M. Layman
National Library of Medicine


-----Original Message-----

From:  Richard.Holland at agresearch.co.nz
Sent:  10/1/2003 05:03:16 PM
To:  <pubmednew at ncbi.nlm.nih.gov>
Subject:  [Pubmednew] Problem with esearch.fcgi

Hi,

I can successfully search Entrez using the web-based forms for the
following term:

XM_055766

However, the same search via the eutils tool esearch.fcgi
(?db=nucleotide&term=XM_055766) returns no results. What's going on?

cheers,
Richard



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Best regards,

Monica L. Romiti
NCBI User Services

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