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

[Simon Twigger]

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