[Biojava-l] Gene Ontology

[Matthew Pocock]

Hi Tim,

It's one of those things that would have been nice to
have a long time ago, but nobody ever wrote. What is
the API for a GO term? I'm wondering if we can just
re-use the Annotation/AnnotationType interfaces and
suck this in as a constrained Map. 

Go terms have an ID and (possibly) a description. By
the isa relationship, they have a (single?) parent and
(possibly no) children. I'm assuming Go has a part-of
relationship (or it's inverse, has-a). What else does
a GO term have?

Then, there are go ontologies, or roots. These have a
root GO term.

We would need some way to map between a set of
database IDs and GO terms - GO -> all IDs with that
term, or perhaps (GO,seqDB) -> all features with that
term.

What have I missed off? What else would you need
API-wise for your GUI to work?

Matthew

 --- "Dudgeon, Tim" <TDudgeon@OSIP.com> wrote: > There
has been mention of a Gene Ontology API and/or
> browser within BioJava
> in the past.
> I've also started off down that route, but before I
> go too far I thought it
> made sense to check whether there was any consensus
> here.
> I don't want to reinvent the wheel yet again and
> will be happy to help get
> something into BioJava.
> 
> What I'd like to see is an API to the GO database
> (probably with adaptors to
> its various forms), plus some gui browser that can
> form a component of a
> bigger tool.
> Browser would probably initially use a JTree type
> appraach, but eventually
> something that better reflected the fact that a GO
> term can have multiple
> parents.
> 
> What's the state of play here?
> 
> Tim
> 
> 
> 
> 
> =======================================
> Dr. Tim Dudgeon
> OSI Pharmaceuticals
> Watlington Road, Oxford,
> OX4 6LT, UK
> tdudgeon@osip.com
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

__________________________________________________
Do You Yahoo!?
Everything you'll ever need on one web page
from News and Sport to Email and Music Charts
http://uk.my.yahoo.com