[ensembl-dev] GRCH37 biomart

Wolf Beat Beat.Wolf at hefr.ch
Mon Aug 28 21:56:02 BST 2017


Thanks, i do know that. I actually use it. Its just that that version is terribly outdated in terms of SNPs etc.


What i wanted to note is that i'm quite sure, that this is a bug and not intended.


That said, i guess i will have to find a different way to differentiate between "good" and "bad" quality genes.


Thank you anyway


Kind regards


Beat Wolf

________________________________
From: Dev <dev-bounces at ensembl.org> on behalf of Thomas Danhorn <danhornt at njhealth.org>
Sent: Monday, August 28, 2017 10:49:33 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] GRCH37 biomart

I did not realize that GRCh37 was actually getting updated rather than
just providing a link to version 75.  If you don't mind the older
annotation (not sure what was actually updated since then), you could use
version 75 at http://feb2014.archive.ensembl.org/biomart/martview/ (or
through the version 75 Perl API) -- the Status field is there, like it
has always been.

Thomas


On Mon, 28 Aug 2017, Wolf Beat wrote:

> 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.
>
>
> Kind regards
>
>
> Beat Wolf
>
> ________________________________
> 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
>
> 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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