[ensembl-dev] GRCH37 biomart

[Thomas Danhorn]

Hi Beat,

As I was informed a couple of days ago, Gene and Transcript Status have 
been retired from BioMart with version 90 and won't return, see 
http://lists.ensembl.org/pipermail/dev/2017-April/012421.html for the 
rationale and details.  I will let more competent people address your 
practical problem, and I am not quite sure what your issue is with GRCh37 
-- being archived, it should not have changed and you should be able to do 
as always.

My guess is you will have to test the e.g. the Ensembl version (GRCh37 is 
75; the first without "Status" is 90) in your script and check the 
relevant field (transcript_status for GRCh37, transcript_tsl for v90 and 
newer), then interpret the results accordingly.

Hope this helps,

Thomas


On Sun, 27 Aug 2017, Wolf Beat wrote:

> Hello,
>
>
> after the latest update of ensembl, some of my scripts stopped working.
>
>
> I noticed that the transcript_status in biomart was removed and replaced 
> with transcript_tsl.
>
>
> Well, not completely. It has only been replaced in the official ensembl 
> version, not grch37. Which means, i have no way right now to know the 
> support level of a transcript in grch37, which is kind of a problem.
>
>
> I could not find a detailed changelog about biomart. Is there any? Where 
> can i be informed about changes to the API (ideally in advance)? Why has 
> the transcript status been removed? Will it be readded (or the tsl 
> information be added? If yes, what is the timeframe?
>
>
> I know, many questions
>
>
> Thank you for your help
>
>
> Kind regards
>
>
> Beat Wolf
>

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