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" <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > 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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
