[Bioperl-l] pubmed

[Yu Zhou]

Thanks!

I am using Bioperl-1.4, not bioperl-live. That may be the reason why
it does not work!



On 5/10/06, Brian Osborne <osborne1 at optonline.net> wrote:
> Qunfeng,
>
> I'm using bioperl-live, I'm able retrieve the single PubMed id found in the
> 56961711 entry using the pubmed() method. Note that there are 4 references,
> only one of which has a Pubmed id. Also, the authors() method prints out the
> authors, not the Pubmed id. If you have a problem please show your code and
> tell us which version of Bioperl you're using.
>
> Brian O.
>
>
> use strict;
>
> use lib "/Users/bosborne/bioperl-live";
>
> use Bio::DB::GenBank;
>
>
>
> my $db = Bio::DB::GenBank->new;
>
> my $seq = $db->get_Seq_by_id(56961711);
>
> my $ann_coll = $seq->annotation;
>
>
> foreach my $ann ($ann_coll->get_Annotations('reference')) {
>
>   print "Author: ", $ann->authors, "\nPubmed id: ", $ann->pubmed, "\n";
>
> }
>
>
>
>
>
> On 5/9/06 9:35 PM, "Yu ZHOU" <zhouyubio at gmail.com> wrote:
>
> > Qunfeng <qfdong <at> iastate.edu> writes:
> >
> >>
> >> Hi there,
> >>
> >> http://bioperl.org/HOWTOs/Feature-Annotation/anno_from_genbank.html
> >>
> >> I am not very familiar with BioPerl. I tried to follow the example
> showing
> >> in the above page to retrieve pubmed ID under each Reference tag , i.e.,
> >> $value->pubmed(), but it doesn't work for me for the seq gi#56961711. The
> >> authors() works for me.  Appreciate any suggestions.
> >>
> >> Qunfeng
> >>
> >
> >
> > Hi,
> >
> > I have the same problem with you. Here is what I have done, by using
> regular
> > expression to match the value of 'location' tag, if there is.
> >
> > #------------------
> > my $ann = $seqobj->annotation(); # annotation object
> > foreach my $ref ( $ann->get_Annotations('reference') ) {
> >     print "Title: ", $ref->title,"\n";
> >     print "Location: ", $ref->location, "\n";
> >     if ($ref->location =~ /PUBMED\s+(\d+)/) {
> > my $pmid = $1;
> > print "PMID: ", $pmid, "\n";
> >     }
> >     print "Authors: ", $ref->authors, "\n";
> > }
> > #------------------
> >
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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>
>
>


--
Best Wishes!

Yu