[ensembl-dev] Lost information in new biomart release

[Beat Wolf]

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[1]> wrote:


I also couldn't get the 71 archive to work. The url should be 
http://apr2013.archive.ensembl.org/biomart/[2]
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









--------
[1] mailto:wolf at fryx.ch
[2] http://apr2013.archive.ensembl.org/biomart/
[3] mailto:Dev at ensembl.org
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