[Bioperl-l] GO path and GO relationships

[Hilmar Lapp]

I'm assuming you have looked at the Bio::Ontology::OntologyI API? Also, 
for GO the underlying engine is SimpleGOEngine.pm which basically 
delegates most functionality to a Graph::Directed instance (see 
Graph.pm from CPAN).

Given the use cases though as you describe them, the GO API is probably 
indeed your best choice. At least what I can say is that none of the 
OntologyI or Graph.pm methods provides a straightforward solution to 
your problems.

	-hilmar

On Wednesday, August 4, 2004, at 04:25  PM, Jason Stajich wrote:

> The GO API is pretty powerful developed by Chris Mungall and others.
>
> http://www.godatabase.org/dev/
> Click on go-perl and go-db-perl to see SYNOPSIS information.
>
>
> -jason
> On Wed, 4 Aug 2004, Law, Annie wrote:
>
>> Hi,
>>
>> I would like to know if there are modules in bioperl that will help 
>> me find
>> the go path, hierarchy corresponding to An input GO id. Also, I would 
>> like
>> to know if there is something in bioperl if given as input a group of 
>> GO
>> identifiers will indicate the
>> Relationship between the GO identifiers ie. Parent or child of or is 
>> a.
>>
>> I am open to using resources available in bioperl db or separate 
>> modules.
>>
>> Thanks very much,
>> Annie.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------