[ensembl-dev] Missing attributes in BioMart for Ensembl version 90

[Thomas Danhorn]

Thank you very much, Magali and Fergal, that is good to know.

Thomas



On Fri, 25 Aug 2017, Fergal wrote:

> Hi Thomas,
>
> To follow on from what Magali said, the transmembrane helices are missing in mouse and human in e90 due to an issue with the protein annotation pipeline. This issue has since been resolved and the transmembrane helices will be back in e91.
>
> You can get most of the data from the e89 archive. That should work for everything bar new genes/transcripts added in e90.
>
> Fergal.
>
>
>
> On 25 Aug 2017, at 08:46, mag <mr6 at ebi.ac.uk> wrote:
>
>> Hi Thomas,
>>
>> The status field for genes and transcripts has been retired, as announced by Andy Yates back in April (http://lists.ensembl.org/pipermail/dev/2017-April/012421.html)
>> The version 90 BioMart is the final product, containing all data generated for release 90.
>>
>>
>> Hope that helps,
>> Magali
>>
>> On 24/08/2017 21:58, Thomas Danhorn wrote:
>>> Hi,
>>>
>>> I noticed that some of the BioMart attributes (specifically in Ensembl Genes -> Mouse Genes) available in previous Ensembl versions are missing in the current version, e.g. "Status (gene)" (under GENE), and "Transmembrane helices" (under PROTEIN DOMAINS AND FAMILIES: -> Protein features).
>>>
>>> Is the version 90 BioMart still a work in progress, or were these attributes removed deliberately?  If the former, when can we expect them to be added, and if the latter, why?
>>>
>>> Thank you very much for your help!
>>>
>>> Thomas
>>>
>>> NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>