[Bioperl-l] Bio::Ontology help solicited

Govind Chandra govind.chandra at bbsrc.ac.uk
Thu Jun 19 10:27:21 EDT 2008


Hi Hilmar,

Thanks for the very quick response.

I changed the line below 

my ($term)=$ontology->find_terms(-name => "GO:0000072");

to 

my ($term)=$ontology->find_terms(-identifier => "GO:0000072");

but it does not make any difference. From perldoc I gathered that -name
and -identifier should do the same thing anyway.

Cheers

Govind



On Thu, 2008-06-19 at 10:07 -0400, Hilmar Lapp wrote:
> I think you want to use -identifier rather than -name if you are  
> querying by an identifier.
> 
> Let us know if that doesn't work either.
> 
> 	-hilmar
> 
> On Jun 19, 2008, at 9:42 AM, Govind Chandra wrote:
> 
> > Hi,
> >
> > In the code snippet below it seems I get the Bio::Ontology::Ontology
> > object $ontology but $ontology->find_terms is failing. It will help
> > greatly if someone points out what is wrong with this code and  
> > suggest a
> > correction. That the obo file is being read is obvious from the time  
> > it
> > takes from invocation to output.
> >
> > I wrote another version of this script which read the "go" format  
> > and it
> > works fine. I cannot use the go format because it is deprecated and  
> > not
> > frequently updated. Even if I am willing to use the go format, the
> > process.ontology file (from geneontology.org) has an error in it which
> > causes Bio::OntologyIO->next_ontology() to fail. It will be best if I
> > could make the obo format work for me.
> >
> > Cheers
> >
> > Govind
> >
> > ### code begins ###
> >
> > use strict;
> > use Bio::OntologyIO;
> >
> > my $file='gene_ontology.1_2.obo';
> > my $parser = Bio::OntologyIO->new(
> >  -format => "obo",
> >  -file => $file
> >  );
> > my $ontology = $parser->next_ontology();
> > print(ref($ontology), "\n");
> > my ($term)=$ontology->find_terms(-name => "GO:0000072");
> > print($term->definition(), "\n");
> > print("$term\n");
> > print(ref($term),"\n");
> >
> > ### code ends ###
> >
> > ### output begins ###
> > Bio::Ontology::Ontology
> >
> >
> > Can't call method "definition" on an undefined value at
> > ontology_check.pl line 26, <GEN0> line 288014.
> > ### output ends ###
> >
> >
> > Other Possibly relevant information:
> > ------------------------------------
> >
> > Perl is: v5.8.8 built for x86_64-linux-thread-multi
> >
> > BioPerl is: bioperl-1.5.2_102
> >
> > Output of uname -a: Linux n61347 2.6.18-92.1.1.el5 #1 SMP Thu May 22
> > 09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
> >
> > Contents of /etc/redhat-release: Red Hat Enterprise Linux Server  
> > release
> > 5.2 (Tikanga)
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



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