[MOBY] [MOBY-l] Core information about biological objects...

[Mark Wilkinson]

Hi Simon, 

I'm just taking a quick stab at an answer to this - off the top of my
head thoughts:

The situation you are describing is very similar to the issue that
Rebecca raised on the list a couple of months ago w.r.t. Arabidopsis
loci (Rebecca: "*our* loci have this this and this special property
associated with them";  Mark: "no, Arabidopsis loci are not more
specialized than Fly loci, so we should design the object to be as
generic as possible and put these special properties in the Xref block")

In my mind, gene symbols are ID's in the same way that gi numbers are
ID's.  They are unique (or supposed to be) within the namespace of a
particular organism.  As such, I think the lightest object you would
have would be something like:

<Object namespace='RGD' id='Abc1'/>

I think we need to build a URL object - it would somehow inherit from
String, but we might need a little more granularity in there somewhere. 
I am loathe, however, to embed a URL in a Locus, Strain, or any other
object that is supposed to represent a biological "thing", since
biological "things" don't have URL's :-)  Moreover, not everyone will
have a URL to associate with a Strain Object, so it becomes a barrier to
other people's use as soon as we put things in the object that are not
"generic" to all organisms.  I'd prefer to have a separate service that
accepts Objects in the RGD namespace and returns the associated URL
objects, or somehow put this URL info into the Cross-Rerence block
rather than building it into the biological data object itself.

Those are my initial thoughts on the subject, but I think we should
discuss it more deeply and document our thoughts on-list since this is
likely going to be a common question for people building new data
Classes...

M

On Thu, 2003-09-18 at 10:13, Simon Twigger wrote:
> Hi there,
> 
> I've been thinking about literature related services using MOBY, in  
> particular how one might be able to query a db to find out what it knew  
> about a particular reference. The idea would be to query a db service  
> asking 'do you have this reference in your system, and if so, what  
> information have you got linked to it?' The service would then return  
> something describing what, if anything, it knew about a reference. In  
> our context at the Rat Genome Database this would be such things as -  
> the genes/rat strains/sequences, etc. that we have curated from the  
> paper.
> 
> ideally you would want the list of 'things' that get returned to be  
> MOBY objects but lightweight as there might be a lot of info for some  
> references and you dont necessarily know what you are interested in  
> (though I suppose this could be an additional parameter in the initial  
> query ("do you have any gene records linked to this reference?")).
> 
> This leads me to wonder what such a lightweight object would look like  
> and what it would contain. You'd like to know it was a 'gene' but you  
> dont want a load of extra info, perhaps just the gene symbol, the db's  
> ID for the gene and perhaps a URL to link in to the report in the  
> database. This should be sufficient to generate a useful report on the  
> reference and give info on how to follow up if you identify specific  
> objects you want to know more about.
> 
> How would one create such an lightweight object in the MOBY environment  
> - use a full blown gene object but only return a limited core attribute  
> set, have a separate lightweight gene object with just these  
> attributes? ideally everyone implementing the service would use the  
> same object and by using a lightweight object with a limited set of  
> standard core attributes it would be useable by everyone and still  
> allow db's to implement a 'heavyweight' object to include their  
> specific attributes, accessible via a different, specific service.
> 
> I notice we have a lightweight Amino Acid object, I'd like to have such  
> things as gene, strain, quantitative trait locus, SSLP (microsatellite  
> marker). What do other people think about such standard objects and  
> what might the core attributes be for them. The trick is to return the  
> smallest amount of useful information that allows a subsequent service  
> or user to know which object they are interested in without having to  
> get the heavyweight objects to find the appropriate attribute. Also, to  
> limit the table joins in the database so the query is fast (can always  
> run off views or specific flat files though).
> 
>   Here are my thoughts, a number of these objects have mapping  
> information though the question then becomes which map coordinates do  
> you want, do you want them all, default to genome position, etc. - the  
> complexity goes up when you add this in and things cease to become  
> lightweight.
> 
> Gene:
> Symbol: Abc1
> ID: 12345
> namespace: RGD
> URL: http://rgd.mcw.edu/query/query.cgi?id=RGD:12345
> 
> [Might also want brief mapping information: chromosome, position?]
> 
> Strain:
> Symbol: BN/SsMCW
> ID: 345346
> namespace: RGD
> URL: http://rgd.mcw.edu/query/query.cgi?id=RGD: 345346
> 
> [Might also want strain type: inbred, outbred, consomic, congenic,  
> recombinant inbred, etc., Im sure there are other terms for the other  
> organisms]
> 
> QTL:
> Symbol: Bp123
> ID: 23453
> namespace: RGD
> URL:  http://rgd.mcw.edu/query/query.cgi?id=RGD: 23453
> 
> [Might also want long name (Blood pressure QTL 123), chromosome]
> 
> SSLP:
> Symbol: D1Rat1
> ID: 65432
> namespace: RGD
> URL: http://rgd.mcw.edu/query/query.cgi?id=RGD: 65432
> 
> [Might also want chromosome, position]
> 
> 
> 
> What do other people think??
> 
> 	Simon
> 
> ------------------------------------------------------------------------ 
> --------------------------
> Simon Twigger, Ph.D.
> Assistant Professor, Bioinformatics Research Center
> 
> Medical College of Wisconsin
> 8701 Watertown Plank Road,
> Milwaukee, WI, 53226
> tel. 414-456-8802, fax 414-456-6595
> 
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-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae