[MOBY-l] Genomic position-based GO search...

[Lincoln Stein]

This is a totally MOBYish thing to do.  One would use a DAS service to 
transform a genomic region into a list of genes, an ontology association 
service to transform the list of genes into the list of GO terms, and an 
ontology tree service to select those terms that descend from a desired root.

Lincoln

On Thursday 21 November 2002 12:49 pm, Simon Twigger wrote:
> Hi there,
>
> (Apologies for the GO/BioMOBY cross post but I think its relevant to
> both)
>
> As part of our ongoing work to implement an ontology schema within RGD
> we were doing some use case analyses and one of the big things I think
> our users (Rat geneticists/genomic people, positional cloners, etc)
> want to do is to find out what genes are in their region of interest
> (defined by a QTL, syntenic region, or similar) and from that, the GO
> terms associated with those genes. The next step would be to build in
> some sort of filter that allowed them to ask "What genes in this region
> are part of XX process/component/function?" etc. Im sure this is
> something that isnt restricted to Rat genomics.
>
> I know that this isnt too hard to build for each individual db as they
> have the gene information, the mapping information and the GO
> information locally and its all integrated. However, when you are doing
> comparative analyses (at least in our case) you know the syntenic
> region you are interested in but you dont have all the
> genes/positions/terms for the other organism(s) in your own database so
> you cant easily offer that functionality. You might not want to bump
> the user off to the other organism db to use their interface (if it
> exists) and this also wouldnt work if you want this functionality
> inside a tool rather than as a user-operated search function.
>
> Im wondering if this is functionality that could be provided either by
> GO, or by a db for their own organism, that others could use thereby
> saving others the hassle of maintaining lots of info about the other
> organisms genes and locations?
>
> Two potential solutions that I thought of:
> Option 1 - add the mapping information into GO: add chromosome and
> genomic location (and presumably build/reference map info). If you then
> know the region you are interested in from the other organism you can
> get all genes with GO terms of interest between START and STOP on
> chromosome N. Downsides to this are adding yet more info to GO files
> and schema, the hassle of keeping things up to date at GO, etc. and it
> might not be worth the pain.
>
> Option 2 - (I like this one) Have a standard API offered by a db
> (webservices/BioMoby would seem to be a good fit here) that others can
> call to extract this information: You pass in the chromosome, the map
> and the region and optionally some GO terms that you want to use to
> refine the returned results and the webservice returns a list of genes
> in that region that match those criteria. On the MOBY front - Im not
> sure if this is violating the atomic input > transform > output concept
> by doing too much in the transform step and it could certainly be
> broken down into component parts and joined back together.
>
> What do others think about this? Ultimately I'd love to see this
> genomic position based search expanded so I could pop a genome browser
> on top to display not every gene/feature/SNP etc. in a region but only
> those that match certain criteria - a genome-based search engine for
> the db.
>
>
> 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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-- 
Lincoln Stein
lstein at cshl.org