[ensembl-dev] Lost information in new biomart release

Rhoda Kinsella rhoda at ebi.ac.uk
Wed Jun 19 18:16:36 BST 2013 

Hi Beat
The missing information has now been added to the Ensembl gene 72 mart database on www.ensembl.org. Thanks again for reporting this.
Regards
Rhoda

On 19 Jun 2013, at 11:07, Beat Wolf <wolf at fryx.ch> wrote:

> Hi Rhoda,
>  
> Thank you for your fast help!
>  
> Regards
>  
> Beat
>  
> On Wednesday 19 June 2013 10.49:23 Rhoda Kinsella wrote:
> Hi Beat
> 
> The Ensembl release 71 archive is now working. Apologies for the inconvenience.
> Regards
> Rhoda
> 
> On 19 Jun 2013, at 09:03, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
> 
> Hi Beat
> We don't produce beta builds of future releases so i'm afraid there is no way to test your pipeline before a release is made live. We make every effort to inform our users about what changes to expect in a future release via our blog. We also extensively test and QC all our data and infrastructure before every release. 
> 
> Unfortunately, as with any project dealing with large volumes of data, some issues do arise. Any issues that are discovered once we release are dealt with as swiftly as possible. I will email as soon as our archive website is back up for release 71 so that you can start your pipeline and we will aim to replace the missing data in the Ensembl gene mart as soon as possible.
> 
> Kind regards
> Rhoda
> 
> 
> 
> 
> On 19 Jun 2013, at 08:11, Beat Wolf <wolf at fryx.ch> wrote:
> 
> Hello Rhoda,
>  
> great to hear that the isse can be fixed today or tomorrow. As i said, quite a lot of code depends on it. If the archive can be fixed even earlier that would be even better.
> For the future, are there any beta builds available of future releases? I would be happy to test my software before the official release to see if anything is broken. As this is the second time in a row a functionallity i depend on disapears, this would be a great way to avoid future problems.
>  
> Best regards
>  
> Beat Wolf
>  
> On Tuesday 18 June 2013 19.52:44 Rhoda Kinsella wrote:
> Hi Beat
> 
> Thank you for reporting these issues. You are correct, we are missing the information you mentioned. We will try to rectify this as quickly as possible but it may take a day or two to generate and add to the live BioMart database. In the mean time, I will report the issue with the archive BioMart to our web team and hopefully you should be able to get the data from there until we reinstate the data. Apologies for any inconvenience caused and thanks again for reporting the bugs.
> Regards
> Rhoda
> 
> 
> On 18 Jun 2013, at 19:13, Beat Wolf <wolf at fryx.ch> wrote:
> 
> I also couldn't get the 71 archive to work. The url should be http://apr2013.archive.ensembl.org/biomart/
> right?
>  
> The changelog doesn't seem to indicate that the functionality i need was removed. Also, in the changelog of Ensembl Genes 72there is this entry:
> -Reinstated PolyPhen prediction and score filters and attributes
>  
> That should go into  Ensembl Variation 72 i guess. Thank you for fixing that by the way, i reported that when 71 got online.
>  
> I hope the functionality lost this time can be recovered before the 73 release in a few months... quite some code depends on it. If at least the archive would work that would be perfect.
>  
> Thank you for your help
>  
> Greetings
>  
> Beat Wolf
>  
> On Tuesday 18 June 2013 19.38:37 Beat Wolf wrote:
> > Hello,
> > 
> > i have a problem. In the new biomart update that just got out, i can't find
> > a way to get the following information on an exon:
> > 
> > 5_utr_start
> > 5_utr_end
> > 3_utr_start
> > 3_utr_end
> > genomic_coding_end
> > cdna_coding_start
> > cds_start
> > cds_end
> > 
> > Did it move to some place else? Where can i find this information? Thank you
> > for your help!
> > 
> > Best regards
> > 
> > Beat Wolf
> > 
> > _______________________________________________
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> 
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge,
> CB10 1SD
> 
> 
> 
> 
> 
> _______________________________________________
> 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/
> 
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge,
> CB10 1SD
> 
> 
> 
> _______________________________________________
> 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/
> 
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge,
> CB10 1SD
> 
> 
> 
> 
> 
> _______________________________________________
> 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/

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD



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