[MOBY-l] Request for BioMoby support letters

[Paul Gordon]

Yes, my "What color are John's eyes?" example was trying to be too 
untechnical perhaps.
Equally as mind-numbing as the Serine Threonine Kinase example when 
you're writing an aptitude test though :-)

> On Thu, 09 Aug 2007 15:02:56 -0700, Paul Gordon <gordonp at ucalgary.ca>  
> wrote:
>
>   
>> The MOBY 2.0 idea (Mark, correct if I'm wrong), is to load up the  
>> appropriate
>> facts (propositions) from services as they are needed to check the truth  
>> of a
>> statement (scientific hypothesis).  These facts are not necessarily from  
>> a database,
>> it could be that a service returns a proposition like "ing1 and yng1 are  
>> orthologs"
>> based on a BLAST you did on your server.  Such a service would be  
>> declared
>> with a signature:
>>
>> "I return facts of the form 'X and Y are orthologs'"
>>     
>
>
> more or less, that's what I'm saying, yes :-)  It's a bit more than that...
>
>
> Let's take this example.  Say I start with a database of raw, unannotated  
> protein sequences.
>
> As a biological researcher, I don't know (and don't care!) what  
> information is or is not in my database, I only care about the question I  
> am asking... so I ask it!  I pose a SPARQL query over this database:
>
> "Select 'Serine Threonine Kinase' where hasInhibitor 'Coumermycin A1'"
>
> Somewhere in the world is an OWL ontology that states:
>
>     Class(Serine Threonine Kinase) is equivalent to
>        Class(Protein) that
>            hasFunctionalAnnotation 'serine-threonine kinase domain'
>
> The Classes in my query are first looked-up against the OWL model and the  
> definition of "Serine Threonine Kinase" is determined.  The Class  
> resrictions of that class are deconstructed, and the system looks up "what  
> Moby Services consume Protein and can provide a hasFunctionalAnnotation  
> property?".  That service is discovered and executed in the same way Moby  
> works now.  A DL reasoner then classifies these proteins into "Serine  
> Threonine Kinase" or "other", and we return to the SPARQL query with our  
> Serine Threonine Kinase's in-hand.  The system then says "what services  
> consume Protein and provide a hasInhibitor property?  This moby service is  
> auto-discovered and auto-invoked using the Serine Threonine Kinase's as  
> input, and they come back with the hasInhibitor property attached to  
> them.  Now the SPARQL query can be completed, by returning those that have  
> the value "Coumermycin A1" attached to them.
>
> so... starting from raw sequence, I was able to discover those sequences  
> that are inhibited by a molecule of interest... and I didn't have to  
> construct the workflow, I simply asked the question :-)
>
> It sounds a bit like black magic, but I am convinced that we can get  
> something similar to this working in the next couple of years!  the  
> details of *how* we're going to do it are in the grant, but I can't make  
> the grant proposal public at the moment...
>
> M
>
>
>