[Bioperl-l] getting pubmed id from genbank files

[Hilmar Lapp]

On Jul 26, 2005, at 7:49 AM, Nathan Haigh wrote:

> -- snip --
> $VAR1 = bless( {
>        'authors' => 'Clauss,M.J. and Mitchell-Olds,T.',
>        'location' => 'Genetics 166 (3), 1419-1436 (2004) PUBMED   
> 15082560',
>        'title' => 'Functional divergence in tandemly duplicated 
> Arabidopsis
> thaliana trypsin inhibitor genes',
>        'tagname' => 'reference'
>      }, 'Bio::Annotation::Reference' );
> -- snip --

This is odd. The PUBMED line should not be concatenated with the 
JOURNAL line. I wonder where this happens and why. Can you download the 
record from NCBI (using the web interface, format 'GenBank', 'Send all 
to file') and then parse it with Bio::SeqIO? If it works then the 
problem must be in the code that deals with the HTTP-response.

	-hilmar


>
> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at duke.edu]
> Sent: 26 July 2005 15:28
> To: Bioperl-l at portal.open-bio.org
> Cc: Nathan Haigh
> Subject: [Bioperl-l] getting pubmed id from genbank files
>
>
>
> Here is part of the synopsis in Bio::Seq:
>
>      foreach my $ref ( $ann->get_Annotations('reference') ) {
>          print "Reference ",$ref->title,"\n";
>      }
>
>   so do $ref->pubmed instead of $ref->title.
>
>
> -jason
>> On Jul 26, 2005, at 6:02 AM, Nathan Haigh wrote:
>>
>>> I want to be able to supply a list of GI's, retrieve the genbank
>>> files and
>>> parse out the pubmed id's.
>>>
>>>
>>>
>>> I know I can do the first steps of retrieving the genbank files
>>> directly,
>>> but how do I get the pubmed id's? I've been playing around with
>>> things and
>>> haven't yet found out if this can be done.
>>>
>>>
>>>
>>> Cheers,
>>>
>>> Nathan
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> Nathan Haigh
>>>
>>> Bioinformatics PostDoctoral Research Associate
>>>
>>>
>>>
>>> Room B2 211
>>>
>>> Department of Animal and Plant Sciences
>>>
>>> University of Sheffield
>>>
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>>>
>>> Sheffield
>>>
>>> S10 2TN
>>>
>>>
>>>
>>> Tel: +44 (0)114 22 20112
>>>
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>>>
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>>>
>>>
>>>
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>> --
>> Jason Stajich
>> http://www.duke.edu/~jes12
>> jason.stajich -at- duke.edu
>>
>>
> --
> Jason Stajich
> http://www.duke.edu/~jes12
> jason.stajich -at- duke.edu
>
>
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------