[ensembl-dev] Chromosome ideogram

[Damian Smedley]

Apologies for the delay Beat. This is all quite obscure as the data is
hidden in an "invisible" Ensembl BioMart dataset that is used under the hood
when you use the karyotype band filters.

The query you need is:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0"
uniqueRows\
 = "0" count = "" datasetConfigVersion = "0.6" >

  <Dataset name = "hsap_karyotype_start" interface = "default" >
    <Attribute name = "name" />
    <Attribute name = "band" />
    <Attribute name = "seq_region_start" />
    <Attribute name = "seq_region_end" />
    </Dataset>
</Query>

Posting this to "www.ensembl.org/biomart/martservice?query=" will give you
all the start and end positions for each chromosome and band

Best wishes
Damian


On Wed, May 11, 2011 at 8:27 PM, Beat Wolf <wolf at fryx.ch> wrote:

> Hello,
>
> Am Mittwoch, 11. Mai 2011, 18:29:31 schrieben Sie:
> > How are you querying it? Direct SQL access or using the BioMart web
> > services?
>
> I'm using biomart directly trough xml queries. From what i know, ensembl
> uses
> mysql, and with java there is only a GPL connector to mysql, which means
> that
> the whole application has to be open sourced. I'm not aware of any other
> way
> access the data.
>
> Cheers
>
> Beat
>
> > Cheers
> > Damian
> >
> > On Wed, May 11, 2011 at 4:02 PM, Beat Wolf <wolf at fryx.ch> wrote:
> > > Thank you for the information. Now i know better what i'm looking for.
> > >
> > > I'm now able to get the karyotype band IDs for a whole chromosome, i
> just
> > > need
> > > to find a way to get the start/stop positions for every band.
> (actually,
> > > i can
> > > only get the bands where at least one gene is present).
> > >
> > > cheers
> > >
> > > Beat
> > >
> > > Am Mittwoch, 11. Mai 2011, um 16:27:53 schrieben Sie:
> > > > Hi,
> > > >
> > > > The Ensembl BioMart has a karyotype dataset and the gene dataset has
> > > > the genes mapped to karyotype bands so you should be able to get what
> > > > you
> > >
> > > need
> > >
> > > > by querying those somehow.
> > > >
> > > > Cheers
> > > > Damian
> > > >
> > > > On Wed, May 11, 2011 at 3:22 PM, ian Longden <ianl at ebi.ac.uk> wrote:
> > > > > This data is stored in the Karyotype table in Ensembl. Biomart is
> > > > > gene centric so may not have this data as the karyotype data is
> > > > > based  on seq regions (chromosomes in this case)
> > > > > I am not an Biomart expert but i could not see anything obvious in
> > > > > martview.
> > > > >
> > > > > -Ian.
> > > > >
> > > > > On Wed, May 11, 2011 at 3:13 PM, Beat Wolf <wolf at fryx.ch> wrote:
> > > > > > Hello,
> > > > > >
> > > > > > i'm using ensembl in an application i'm writing. It's a java
> > > > > > application
> > > > >
> > > > > and
> > > > >
> > > > > > for that reason i access the ensembl data trough BioMart.
> > > > > >
> > > > > > Now my question. Ensembl has those chromosome ideograms that are
> > >
> > > shown
> > >
> > > > > > on
> > > > >
> > > > > the
> > > > >
> > > > > > website. I would love to integrate such a ideogram in my
> > > > > > application, but
> > > > >
> > > > > i
> > > > >
> > > > > > didn't find a way to access the needed data trough biomart. I'm a
> > > > >
> > > > > computer
> > > > >
> > > > > > scientist, so i might simply not know the right terminology for
> > > > > > what i'm searching for.
> > > > > >
> > > > > > Thank you very much for your help
> > > > > >
> > > > > > Beat Wolf
> > > > > >
> > > > > > _______________________________________________
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> > > > >
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> > > > >
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> > > > >
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>
>
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