[ensembl-dev] Changes in EMBL file format?

[Fin Swimmer]

Hey Anne and Matthew,
thank you for your detailed answer. Is there a place where I can follow
these discussion or how can I be warned if something in the fileformat
have changed?

fin swimmer
Am 15.06.2017 um 10:37 schrieb Matthew Laird:
> Hi Fin,
>
> The discussion about this change began in the context of Genbank files, 
> however since our Genbank and EMBL file dumpers share a common code base 
> the change rippled to the EMBL files as well.
>
> As Anne indicated, this stemmed from wanting to be more INSDC compliant, 
> /note just didn't seem like the appropriate place to put the primary 
> identifier for a record, it's more than just a "note." Unfortunately in 
> the INSDC standards for Genbank files there is no /transcript_id record, 
> despite some other sources using it. /standard_name seemed like the most 
> appropriate choice of those allowed.
>
> But yes, for CDS records, not having a /transcript_id, how do we point 
> to that record's parent. The parent transcript isn't the /standard_name, 
> so a difficult choice was made to stick with the /note field in this 
> context. This does feel like an inconsistency, but we believe the 
> benefit of a transcript having it's primary, stable identifier more 
> prominently part of the record outweighs this negative.
>
> If you have any other questions or concerns, please do let us know.
>
> On 15/06/17 05:25, Fin Swimmer wrote:
>> Hello,
>>
>> I often export gene informations from ensembl in the EMBL file format. I
>> realized that, since the last ensembl update, the transcript id's now
>> have the key /standard_name in the mRNA or misc_RNA part, whereas in the
>> CDS part /note="transcript_id= is still used.
>>
>> Is this change a bug or a feature?
>>
>> fin swimmer
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