[ensembl-dev] e67 mart builder files

[Kiran Mukhyala]

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/<http://www.ebi.ac.uk/%7Erhoda/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.
>>>
>>>
>> _______________________________________________
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>>
>>
>>
>>
>>   --
>> 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
>
>
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