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

[Evelyn Camon]

Hi

>What genes in this region
>are part of XX process/component/function?" etc.

For your information you can find the location of human genes mapped to a
particular GO term using ensembl GO-View.
I'm sure they will extend it for mouse data.

See:http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

Evelyn



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