[Bioperl-l] MeSH term retrieval

Brian Osborne osborne1 at optonline.net
Mon Mar 27 16:47:59 EST 2006


Michael,

Your query was correct, the problem was that that particular entry has a
long, multi-line description which Bio::DB::MeSH couldn't handle. This is
fixed now in bioperl-live. Either install a brand new Bioperl or just copy
the latest Bio/DB/MeSH.pm.

Brian O.


On 3/26/06 7:26 AM, "Michael Seewald" <mseewald at gmail.com> wrote:

> Dear Bioperl-Users, dear Heikki,
> 
> I am trying to retrieve MeSH term descriptions using Bio::DB::MeSH (bioperl
> v1.5.0). Sometimes it works (first example below), sometimes it does not
> (second example). Is there anything wrong with the query?
> 
> Thanks & bets wishes,
> Michael
> 
> 
> use Bio::DB::MeSH;
> 
> my $mesh = new Bio::DB::MeSH();
> 
> # works, compare:
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=MeSH&cmd=search&term
> =Eisenmenger%20Complex
> my $term = 'Eisenmenger Complex';
> print "Term: $term\n";
> print "Desc: ",$mesh->get_exact_term($term)->description,"\n";
> 
> # does not work, compare:
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=MeSH&cmd=search&term
> =Sinus%20Thrombosis,%20Intracranial
> my $term = 'Sinus Thrombosis, Intracranial';
> print "Term: $term\n";
> print "Desc: ",$mesh->get_exact_term($term)->description,"\n";
> 
> 
> --
> Dr. Michael Seewald
> Bioinformatics
> Bayer HealthCare AG
> 
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