Re: [SO-devel] GFF3 Specification

[Anja T. <an...@eb...>]

Hello,
two comments regarding ensembl GVF dumps:

1) In our Ensembl GVF dumps we provide ##sequence-region directives for each seqid. For human this would be:
##sequence-region 1 1 249250621
##sequence-region 2 1 243199373
##sequence-region 3 1 198022430
..
It is not intended to split a chromosome further and if there is a GVF file where this is the case please let me know.

2) I will revise data where we have "Variant_seq=INSERTION" or "Variant_seq=(11 BP INSERTION)" for the next release.
The specification is clear in how the the Variant_seq attribute should be formatted.

Best,
Anja
Ensembl Variation
  
On 26 Feb 2013, at 21:59, Joachim Baran wrote:

> 
> On 2013-02-26, at 4:37 PM, Peter Cock <p.j...@go...> wrote:
>> The fact that Joachim Baran commented that he'd noticed
>> this in GVF data from Ensembl suggests this is more than
>> just a hypothetical usage, and it could be premature to ban
>> in the new revision of GFF3.
>  It should be closely reviewed though. Ensembl's GVF files do not adhere to the GVF specification very well. For example, their variant sequences contain attributes such as "Variant_seq=INSERTION" and "Variant_seq=(11 BP INSERTION)".
> 
>  Either there is a lack of expressiveness in GVF that forces Ensembl to violate the specification in that way, or there is a lack of clearness in the specification's text. (Well, or I get the specification wrong myself...)
> 
> Best,
> Joachim
> 
> 
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