[Bioperl-l] Bio::Ontology support for several indentifiers per term

Pär Engström Par.Engstrom at cgb.ki.se
Wed Jan 21 06:10:51 EST 2004

Hi BioPerl developers,

In the Gene Ontology, some terms have multiple identifiers. E.g. "ATPase
activity" has identifiers GO:0016887 and GO:0004002. However, it seems
that the Bio::Ontology modules only support one identifier per term. 

Consider the following script (using bioperl 1.4):

use Bio::OntologyIO;
my $go_in = Bio::OntologyIO->new
    ( -format => "go",
      -defs_file => "GO.defs",
      -files => ["component.ontology",
		"process.ontology" ]);
my $gene_ontology = $go_in->next_ontology();
print scalar($gene_ontology->find_terms("GO:0004002")), " ";
print scalar($gene_ontology->find_terms("GO:0016887")), "\n";

The output is "0 1", i.e. the term can only be found from one of its

If this is a known issue in Bio::Ontology, is there some way to retrieve
terms by their "secondary" identifiers?


Par Engstrom
Graduate student, CGB, Karolinska

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