On 3/29/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote: > On Thu, 29 Mar 2007, Matt wrote: > > > We have been working on > > trying to integrate explicitly with biopax (http://www.biopax.org/ > > states and generics proposal - level 2 was too limiting) in the hope > > that other databases (like GO, reactome, KEGG, DIP, signalling > > gateway, etc) get dragged along too. Some seem to be. > > BioPAX annotatation scheme is very fragile and in practise almost > unusable.
How is that? > The cross-ref are free forms, and as a consequence, Bob > cannot read the annotation added by Alice. BioPAX developers are aware of > that, and are now moving to a URI-based systems. Cf. the work of Alan > Ruttenberg > http://biopaxwiki.org/cgi-bin/moin.cgi/UriCvNamespaceProposalJune2006 That was always going to wash out in practice. I'm not sure a rule for generating the URI is useful in the long run, especially if these database produce their own URI scheme, then it becomes a less simple task to match other data resources that don't use the biopax scheme to the ones that use the originating databases scheme. > > > -- > Nicolas LE NOVERE, Computational Neurobiology, > EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK > Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074 > http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: [EMAIL PROTECTED] > _______________________________________________ > cellml-discussion mailing list > [email protected] > http://www.cellml.org/mailman/listinfo/cellml-discussion > _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
