Re: [Gmod-ajax] Feature Mark Up

[Ian H. <ih...@be...>]

Chris Mungall mentioned something a while back about some sort of  
universal markup language he & Seth had specced out for GO. He also  
suggested some kind of protocol for publishing feature annotations in  
a sort of universal ontology framework.

Chris, are you on this list? it'd be good to get these & related  
ideas in more concrete form...

As well as rich pop-up info, we need to develop client-server  
protocols for (i) search and (ii) annotation upload.


On Nov 16, 2006, at 8:46 AM, Scott Cain wrote:

> 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  
>> 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  
> 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  
> 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/? 
> start=101357;stop=121356;ref=MAL12;width=800;version=100;label=Annotat 
> edGenes-SyntenySpansVivaxMC- 
> SyntenyGenesVivaxMC;id=9cf36ae32368b7ec3e3c516c08c358d4
>
> which is done with this conf file:
>
> http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/ 
> SynView/gbrowse.conf/plasmodb.conf? 
> revision=1.1.2.1&view=markup&pathrev=gbrowse-session
>
> Scott
>
> -- 
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> --
> Scott Cain, Ph. D.                                          
> ca...@cs...
> GMOD Coordinator (http://www.gmod.org/)                      
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> Cold Spring Harbor Laboratory
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