[ensembl-dev] Lost information in new biomart release

[Beat Wolf]

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[1]> 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[2]> 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/[3]
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.
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