[Bioperl-l] annotations of genes

Chris Mungall cjm@fruitfly.bdgp.berkeley.edu
Fri, 8 Mar 2002 11:30:01 -0800 (PST)

There is a perl-api to the GO database; see http://www.godatabase.org/dev

You can write a script like this:

$apph = GO::AppHandle->new();

# fetch all genes named CDK5
$products = $apph->get_products({symbol=>"CDK5"});

$terms = $apph->get_terms({products=>$products});
foreach my $term (@$terms) {
  printf "%s %s %s\n", $term->public_acc, $term->name, $term->description;

I've been promising an ontology framework for bioperl for a while; though
I'm beginning to think a sufficiently generic framework would have no bio
specific stuff in it anyway so I don't know if bioperl is the right

On Fri, 8 Mar 2002, Guoneng Zhong wrote:

> Hi,
> Broad question.  Is there a way using bioperl mods that I can see what a 
> gene, like, say, CDK5, does?  Perhaps an interface to the GO database?
> G
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