how to create the dataset of the biomart from the ensembl core databases

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how to create the dataset of the biomart from the ensembl core databases

Wenyan NONG
Dear mart-dev,

I have loaded my genomes sequences and genes annotations into the core database from scratch, and then I would like to do some data mining using biomart, how can I create the dataset of the biomart from these core databases, or I should do it manually and one bye one, using MartBuilder and MartEditor. Is there any instruction for that? I am using ensembl 57 and biomart 0.7.

I have been asking for help in ensembl-dev mail list, but have no lucky. Any advice would be appreciated!

Thank you very much!

Best,
Wenyan
CUHK, HK.
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Re: how to create the dataset of the biomart from the ensembl core databases

Richard Holland
It's not an easy task unfortunately - the full process for Ensembl includes a complex series of steps involving MartBuilder and MartEditor that can take a couple of days to complete. As far as I know it's not publicly documented anywhere. If you can find their contact details (Googling works) then Rhoda Kinsella is the person to talk to at the EBI as she is (or at least used to be) in charge of building the Ensembl marts each release.

cheers,
Richard

On 2 Jul 2010, at 09:43, Wenyan NONG wrote:

> Dear mart-dev,
>
> I have loaded my genomes sequences and genes annotations into the core database from scratch, and then I would like to do some data mining using biomart, how can I create the dataset of the biomart from these core databases, or I should do it manually and one bye one, using MartBuilder and MartEditor. Is there any instruction for that? I am using ensembl 57 and biomart 0.7.
>
> I have been asking for help in ensembl-dev mail list, but have no lucky. Any advice would be appreciated!
>
> Thank you very much!
>
> Best,
> Wenyan
> CUHK, HK.

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [hidden email]
http://www.eaglegenomics.com/

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Re: how to create the dataset of the biomart from the ensembl core databases

Wenyan NONG
In reply to this post by Wenyan NONG
Dear Joachim,

I am following the guide in your blog to construct the biomarts from my ensembl databases. I meet some confuse and need your help.

I would like to know how to get the XML-files for creating marts relating to other Ensembl version, just as mart_55.zip/mart_53.zip mentioned in your blog. I have checked the EBI FTP and also googleing but have no lucky, please give me some advice. I am using Ensembl version 57, and maybe update to last version later.

Thank you very much!

Best,
Wenyan
CUHK, HK.


On Fri, Jul 2, 2010 at 4:59 PM, Joachim Baran <[hidden email]> wrote:
Hi Wenyan,

 Perhaps this helps you: http://bergmanlab.smith.man.ac.uk/?p=35

 You can use the XML-files provided in that blog-post and update the
database schemata as described in the post (just a click in
MartBuilder). That should give you an Ensembl mart very close to the
one online.

Best Wishes,
Joachim

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