>>>>> "Tim" == Dudgeon, Tim <[EMAIL PROTECTED]> writes:
Tim> There has been mention of a Gene Ontology API and/or browser Tim> within BioJava in the past. I've also started off down that Tim> route, but before I go too far I thought it made sense to check Tim> whether there was any consensus here. I don't want to reinvent Tim> the wheel yet again and will be happy to help get something Tim> into BioJava. Tim> What I'd like to see is an API to the GO database (probably Tim> with adaptors to its various forms), plus some gui browser that Tim> can form a component of a bigger tool. Browser would probably Tim> initially use a JTree type appraach, but eventually something Tim> that better reflected the fact that a GO term can have multiple Tim> parents. Tim> What's the state of play here? It depends on how you want to represent GO. DAGEdit already contains an API for representing GO, and adaptors for the database, and some of the GO syntaxes. You should be able to pull these out and use them directly as libraries. Alternatively, if you want to use more generic technology, you could use some of the DAML+OIL/OWL API's, which are more than capable of representing the GO DAG, then there are various tools and API's around for representing these, as well as gui tools, or indeed editing environments (such as Oiled (http://oiled.man.ac.uk) for instance...). It's probably also worth reading the Ontology thread on the bioperl list. It's a moot question how much of a GO representation you put into biojava. It might make more sense to use a more generic DAG representation, so that you get, for example, transitive closure, or shortest path stuff for free. Cheers Phil _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
