[Bioperl-l] MeSH term retrieval

t-nakazato at muj.biglobe.ne.jp t-nakazato at muj.biglobe.ne.jp
Mon Mar 27 11:37:18 EST 2006


Hi.

I tried your script with some MeSH Terms.

I can retrieve correct result with "Insulin", but I can't get with
"Insulin, Isophane".

You can't get the result because second example contain "," and
Bioperl don't treat "," correctly, I think.

Takeru


-----
Takeru Nakazato     t-nakazato at muj.biglobe.ne.jp



> Right, but it's all I could find out. The output on my system is:
> 
> $ ./test.pl
> Term: Eisenmenger Complex
> Desc: Defect of the interventricular septum with severe pulmonary
> hypertension, hypertrophy of the right ventricle, and latent or overt
> cyanosis.
> Term: Sinus Thrombosis, Intracranial
> Desc:
> 
> Using Data::Dumper, I found out, that the first mesh object has a key value
> pair for "description", the object from the second query does not. This may
> be pointing at a parsing problem. Any hints welcome.. Could anyone run the
> script on their system and see whether it works in a different setting?
> 
> Best wishes,
> Michael
> 
> 
> On 3/27/06, Hilmar Lapp <hlapp at gmx.net> wrote:
> >
> > There's no psychics on this list AFAIK - if you don't post the error
> > message or further qualify 'does not work' then I'm afraid you won't
> > get much help ...
> >
> > On Mar 26, 2006, at 4:26 AM, Michael Seewald 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.  Seewald
> > > Bioinformatics
> > > Bayer HealthCare AG
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > >
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> >
> >
> 
> 
> --
> Dr. Michael Seewald
> Bioinformatics
> Bayer HealthCare AG
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



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