[Bioperl-l] MeSH term retrieval

Michael Seewald mseewald at gmail.com
Mon Mar 27 06:58:01 EST 2006


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. 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
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>


--
Dr. Michael Seewald
Bioinformatics
Bayer HealthCare AG



More information about the Bioperl-l mailing list