Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

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

Yes, I think that if you provide the ability to represent arbitrary sets 
of features (which the divbrowser was clearly born to do) and an API 
that is mashup/plugin friendly, then we could inch our way towards 
something like this without forgetting that the G in GBrowse stands for 
Generic -- i.e. without doing something that is too specific to one 
particular database.

And yes, I am guiltier than anyone of tossing random ideas into the mix 
  -- really this is blue-sky discussion and should not be confused with 
the more modest, concrete & well-defined goals that we have put in 
writing elsewhere (in our proposal to NIH, on the wiki, etc.)




Chris Mungall wrote:
> On Aug 24, 2007, at 5:41 PM, Mitch Skinner wrote:
> 
>> Ian Holmes wrote:
>>> How would this compare with existing systems e.g. Ensembl MART?
>>>
>> I've only spent a bit of time with it, but I don't see a way to  
>> view the
>> results of a biomart query in the genome browser, which is what I was
>> thinking.  In addition to creating new tracks by uploading, we could
>> allow people to create tracks by defining queries.  It should be easy
>> for us to track how popular these are, so there's a natural connection
>> to the points and feedback/recognition items from the game/webapp  
>> article.
>>
>> Also, while you can specify a list of IDs to biomart, that requires  
>> the
>> user to manage their own collection.  We could certainly make  
>> collection
>> management a lot easier (e.g., an "add this to my collection"  
>> button on
>> feature popups).  Centralizing collections also makes them easier to
>> share (like the "post your hotlist" thing, with individual features
>> instead of tracks).
> 
> I like this idea, but in the interests of not seeing us diverge too  
> far from the core plan I'd like to place this in the context of a  
> wider architecture.
> 
> I think GBrowse-ajax should make the assumption that we will soon  
> live in an ideal bioinformatics nation where data sources will expose  
> powerful query interfaces - MART, InterMine, or more ontology-based  
> schemes - through some appropriate HTTP API or RESTful architecture.
> 
> GBrowse should provide a way of slurping a bunch of feature IDs and  
> showing them in an appropriate way. Or, conversely, a way of  
> exporting a bunch of IDs, perhaps from a ROI.
> 
> So long as gbrowse is mashup/plugin friendly then it should be  
> possible to wrap this functionality in the way you describe.
> 
>> In addition to having a nice query building UI like biomart does, I
>> think it makes sense to expose something lower level, like (say) raw
>> SPARQL.  Most biologists won't use it, but if we make it easy for more
>> advanced users to share their queries with other people then it's  
>> still
>> pretty useful IMO.
> 
> SPARQL is fairly limited. However, it is the standard query language  
> for RDF.
> 
> You can assume that a SPARQL wrapper for Chado will be available  
> sometime in the next half of year or so. We've already done this for  
> the GO database[1]. Again, I think GBrowse should just worry about  
> accepting lists of IDs and/or regions - this would be the main point  
> of contact. Some enterprising semweb fan will then hopefully cobble  
> together a non-horrible SPARQL interface that pipes the results into  
> a GBrowse display.
> 
>> But these are all just random ideas.  Mainly, I wanted to ask for help
>> translating game ideas into stuff that relates more concretely to what
>> we're doing.
>>
>> Mitch
>>
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