Re: [Gmod-ajax] Feature Mark Up

[Scott C. <ca...@cs...>]

Actually, what I wrote before isn't quite correct; while the gbrowse cgi
doesn't server up raw information, other cgis in the gbrowse
distribution can.  You can get both DAS1 and biomoby, though I don't
know that much the details of what the streams look like (DAS2 is XML, I
don't think DAS1 is).  It is possible that javascript client-side code
is already written for these services, I just don't know about it.

Scott


On Thu, 2006-11-16 at 09:54 -0800, Ian Holmes wrote:
> Chris Mungall mentioned something a while back about some sort of =20
> universal markup language he & Seth had specced out for GO. He also =20
> suggested some kind of protocol for publishing feature annotations in =20
> a sort of universal ontology framework.
>=20
> Chris, are you on this list? it'd be good to get these & related =20
> ideas in more concrete form...
>=20
> As well as rich pop-up info, we need to develop client-server =20
> protocols for (i) search and (ii) annotation upload.
>=20
>=20
> On Nov 16, 2006, at 8:46 AM, Scott Cain wrote:
>=20
> > On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
> >> Hi Andrew,
> >>> Next comes the figuring out how to populate the pop up menu with
> >>> relevant info...
> >>>
> >>>
> >> Yep. This is more tricky... I think we should try and use as many
> >> 'official' GBrowse calls as possible to ensure future =20
> >> compatibility. I
> >> wonder if Lincoln or Scott (if they are reading this) could offer any
> >> advice?
> >>
> > The GBrowse cgi doesn't expose much in terms of fundamentals that one
> > could use for populating popup menus with data.  Currently, people who
> > use popups with gbrowse create all of the data up front and encode =20
> > it in
> > javascript elements in the imagemap.  I suppose that works fine from a
> > cgi point of view, but is not as appropriate for an ajax =20
> > application (is
> > it?).  So if we want to make it work in an 'ajaxy' way, we'll need
> > either to expand the api of the gbrowse cgi, or create another cgi for
> > serving up xml for requests like that.
> >
> > If you want to see an example of how people are currently generating
> > popups, you can look at this example:
> >
> > http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/?=20
> > start=3D101357;stop=3D121356;ref=3DMAL12;width=3D800;version=3D100;labe=
l=3DAnnotat=20
> > edGenes-SyntenySpansVivaxMC-=20
> > SyntenyGenesVivaxMC;id=3D9cf36ae32368b7ec3e3c516c08c358d4
> >
> > which is done with this conf file:
> >
> > http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/=20
> > SynView/gbrowse.conf/plasmodb.conf?=20
> > revision=3D1.1.2.1&view=3Dmarkup&pathrev=3Dgbrowse-session
> >
> > Scott
> >
> > --=20
> > ----------------------------------------------------------------------=20
> > --
> > Scott Cain, Ph. D.                                         =20
> > ca...@cs...
> > GMOD Coordinator (http://www.gmod.org/)                     =20
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> > ----------------------------------------------------------------------=20
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>=20
>=20
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory