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

[Heikki Lehvaslaiho]

Richard,

If you look carefully at the entry XM_055766 in the Entrez server, you
notice this:

COMMENT     MODEL REFSEQ:  This record is predicted by automated  
            computational analysis. This record is derived from an 
            annotated genomic sequence (NT_024812) using gene 
            prediction method: BLAST, supported by mRNA and EST 
            evidence.

It is not a GenBank entry although it looks like one and NCBI Entrez
claims it is one but in fact it is from the RefSeq database. 

The XP_* entries can not be retrieved using Bio::DB::RefSeq, either,
because it fetches entries from EBI copy of the datebase which doeas not
contain all the latest sequence subclasses (only NC_*, NT_*, NM_*,
NP_*). I'll try to get that updated.

	-Heikki



On Tue, 2003-10-07 at 14:58, Holland, Richard wrote:
> 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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> 
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> 
> Best regards,
> 
> Monica L. Romiti
> NCBI User Services
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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