On 2 Aug 2010, at 10:45, Jonathan Warren wrote: > I'm not sure I agree with returning all annotations for every tiny part of a > sequence requested. > If you consider DAS to be used for visual display mainly - then it seems a > bit ridiculous to return all publications related to a segment (take a case > where you have many publications related to a protein sequence). If > publications aren't asked for i.e. non-positional annotations then I don't > think they should be given. So I guess I'm agreeing with Jim here. > > Given the history of DAS I would propose a non-positional parameter as > apposed to "positional". > > I think we have to remember that the 1.6 spec is supposed to mainly be a > consolidation of the way DAS is being used and DAS is supposed to be simple > (or not overly technical and difficult to pick up anyway). However- obviously > we don't want to propagate practices that really don't make sense. The 0,0 > thing is a hack like we had hacks for ontologies which now for 1.6 we have > cvIds (I think are a big improvement). So we need something that is simple > and obvious for a big all encompassing thing like positional vs > non-positional.
I'm not quite sure what you're suggesting we do in 1.6? > > > > On 2 Aug 2010, at 09:50, Leyla Garcia wrote: > >> *Hi list, >> >> *>No magic numbers. >> >> *According to discussions on this matter, I will change MyDas behaviour so 0 >> will be no >> "magic number" any more, >> >> *>Types can be used for filtering, and actually you get more fine-grained >> control than simply positional or non-positional. (I use this technique now >> in DASher.) * >>> In my opinion, the current spec as written is correct. That is, >>> non-positional features don't just apply to the whole sequence, they apply >>> to any part of the sequence. >>> As an example, consider a journal reference --- a particular protein was >>> isolated by a lab, they wrote a paper about it, and deposited the protein >>> sequence in a database. If you look at a subsequence of the protein >>> sequence, that subsequence still derives from the paper, right? So >>> therefore the feature containing that journal reference should still be >>> attached to the subsequence. >>> On that basis, I think the uniprot server is technically doing it wrong and >>> should be changed, although I have to say that in practice it hasn't been >>> an issue for me. >> >> *and non-positional features will be always returned. >> Since UniProt is built upon MyDas, its behaviour will change as well. >> >> Thanks, >> >> Leyla >> * >> >>> >>> Dave >> >> _______________________________________________ >> DAS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/das > > Jonathan Warren > Senior Developer and DAS coordinator > blog: http://biodasman.wordpress.com/ > [email protected] > Ext: 2314 > Telephone: 01223 492314 > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a > charity registered in England with number 1021457 and acompany registered in > England with number 2742969, whose registeredoffice is 215 Euston Road, > London, NW1 2BE._______________________________________________ > DAS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/das _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
