[ensembl-dev] e67 mart builder files

[Thomas Maurel]

Dear Kiran,

You are right, the canonical transcript stable id is no longer available in BioMart as the changes made to the core schema (merging of the stable_id tables with their parent tables) made it impossible to add this data using the martbuilder tool. 

Hope this helps,

Regards,
Thomas

On 11 Jul 2012, at 00:08, Kiran Mukhyala wrote:

> Hi Thomas,
> Thanks for the MTMP SQLs. 
> 
> One more question - 
> 
> The attribute canonical_transcript_stable_id has been missing from the Ensembl BioMart since e65. Is this attribute no longer supported?
> 
> -Kiran
> 
> On Mon, Jul 9, 2012 at 8:49 AM, Thomas Maurel <maurel at ebi.ac.uk> wrote:
> Hi Kiran,
> 
> I am sorry, I forgot to mention that we are now using these MTMP tables to help us build the ensembl, snp and functional genomics marts.
> You will have to create them before updating the mart schema.
> 
> 1) MTMP_probestuff_helper tables for the Ensembl mart: 
> This table need to be built for all the funcgen databases.
> You can use the iterate_tables.ksh script to iterate over multiple species databases and use the probestuff_helper.sql file to create this table in each database.
> 2) Variation views for snp mart and Ensembl mart :
> You will need to run the variation_views.sql and the structural_variation.sql files for all the variation databases using the iterate_tables.ksh script.
> 3) eFG views for Functional genomics mart:
> The functional genomics views and tables are created for all the funcgen databases using the iterate_tables.ksh script.
> 
> Please find the sql files and the iterate_tables.ksh script at the following location:  http://www.ebi.ac.uk/~maurel/mart_prebuild_patches/
> 
> Hope this helps,
> Regards,
> Thomas
> On 9 Jul 2012, at 06:40, Kiran Mukhyala wrote:
> 
>> Thanks Thomas for the mart builder files.
>> 
>> It looks like the Ensembl Mart building process has introduced usage of new tables like MTMP_transcript_variation and MTMP_probestuff_helper, etc.
>> Would you please explain how to generate these tables? If its documented anywhere, please do point me to it.
>> 
>> Thanks,
>> -Kiran
>> 
>> On Sat, Jun 30, 2012 at 1:59 AM, Thomas Maurel <maurel at ebi.ac.uk> wrote:
>> Hi Kiran,
>> 
>> Please find the martbuilder xmls for release 67 at the following location : 
>> http://www.ebi.ac.uk/~maurel/v67_xml/
>> 
>> Regards,
>> Thomas
>> 
>> On 29 Jun 2012, at 18:28, Kiran Mukhyala wrote:
>> 
>>> Hi Rhoda,
>>> 
>>> Could you please provide the e67 core, funcgen and variation martbuilder files?
>>> 
>>> Thanks,
>>> -Kiran
>>> 
>>> On Wed, Jan 11, 2012 at 3:16 AM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
>>> Hi Kiran
>>> I have provided the files you requested for release 64 and release 65 at the following location:
>>> 
>>> http://www.ebi.ac.uk/~rhoda/v64_v65_xml/
>>> 
>>> Regards
>>> Rhoda
>>> 
>>> 
>>> On 9 Jan 2012, at 19:46, Kiran Mukhyala wrote:
>>> 
>>>> Hello Ensembl BioMart Team,
>>>> 
>>>> Could you please provide the e64 core, funcgen and variation martbuilder files?
>>>> 
>>>> Thanks,
>>>> -Kiran
>>>> 
>>>> On Mon, May 9, 2011 at 5:38 AM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
>>>> Hi Kiran
>>>> You can find the files you need at:
>>>> 
>>>> http://www.ebi.ac.uk/~rhoda/v62_xml/
>>>> 
>>>> Regards
>>>> Rhoda
>>>> 
>>>> 
>>>> On 7 May 2011, at 04:08, Kiran Mukhyala wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> I'd like to upgrade my mart to e62, could you please provide the e62 core, funcgen and variation mart builder files?
>>>> 
>>>> Thanks,
>>>> -Kiran
>>>> 
>>>> Rhoda Kinsella Ph.D.
>>>> Ensembl Bioinformatician,
>>>> European Bioinformatics Institute (EMBL-EBI),
>>>> Wellcome Trust Genome Campus,
>>>> Hinxton
>>>> Cambridge CB10 1SD,
>>>> UK.
>>>> 
>>>> 
>>> 
>>> Rhoda Kinsella Ph.D.
>>> Ensembl Production Project Leader,
>>> European Bioinformatics Institute (EMBL-EBI),
>>> Wellcome Trust Genome Campus, 
>>> Hinxton
>>> Cambridge CB10 1SD,
>>> UK.
>>> 
>>> 
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>> 
>> 
>> 
>> --
>> Thomas Maurel
>> Bioinformatician - Ensembl Production Team
>> European Bioinformatics Institute (EMBL-EBI)
>> 
>> Wellcome Trust Genome Campus, Hinxton
>> Cambridge - CB10 1SD - UK
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> 
>> 
> 
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
> 
> 
> 
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
> 
> 

--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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