[ensembl-dev] GRCH37 biomart
danhornt at njhealth.org
Mon Aug 28 16:13:08 BST 2017
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
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,
On Sun, 27 Aug 2017, Wolf Beat wrote:
> 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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