[ensembl-dev] GRCH37 biomart
Beat.Wolf at hefr.ch
Mon Aug 28 19:32:34 BST 2017
Thank you very much, especially for the link to the discussion where this was decided.
That said, GRCH37 is missing both Status and tsl, which means, its neither like the old nor the new version of biomart.
GRCH37 is also at version 90, which makes it not possible to use the version info as an indication if the feature is available or not.
I'm now using the "gencode basic" field as a replacement for the moment, but i'm not super happy about that. But at least it does give similar results.
From: Dev <dev-bounces at ensembl.org> on behalf of Thomas Danhorn <danhornt at njhealth.org>
Sent: Monday, August 28, 2017 5:13:08 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] GRCH37 biomart
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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