[Bioperl-l] Bio::Ontology help solicited

Hilmar Lapp hlapp at gmx.net
Thu Jun 19 10:50:57 EDT 2008


On Jun 19, 2008, at 10:27 AM, Govind Chandra wrote:

> I changed the line below
>
> my ($term)=$ontology->find_terms(-name => "GO:0000072");
>
> to
>
> my ($term)=$ontology->find_terms(-identifier => "GO:0000072");

That's odd. Did you convince yourself that a term with this identifier  
is indeed in the ontology? If you iterate over all terms (using e.g.  
$ontology->get_all_terms()), is there a term with this identifier?

E.g.: print join("\n", map { $_->identifier; }
                            (grep { $_->identifier =~ /0000072/; }
                                  $ontology->get_all_terms())),"\n";

Does this print anything?

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


I'm not sure where you gathered that from. Could you point me to the  
location that says that?

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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