[ensembl-dev] Source of refseq data in otherfeatures

[Daniel Barrell]

Hi Reece,

There may have been some confusion about your question to the list. 
Hopefully I can clear it up a little.

There are 25,268 "refseq_human_import" genes in the human otherfeatures 
database. These are incorporated into the database from GFF files which 
NCBI provide to us, we do not download them from a public location. We 
do not have the NCBI sequence, only the coordinates of the genes.

The current otherfeatures data dates from refseq_54 (you can see this in 
gene.db_version). We only update this set when NCBI and EnsEMBL do a 
comparison of data sets as part of the CCDS consortium.

Dan


On 04/06/13 02:22, Reece Hart wrote:
> Greetings-
>
> I'm trying to gauge whether ensembl might provide a kinder, gentler 
> interface to refseq data than that provided by EUtils.
>
> What's the source of the refseq data in otherfeatures?
>
> How current is the otherfeatures data?
>
> What reconciliation is done when there are substitutions (e.g., VHL, 
> TNFRSF10C, SERPINE2) or indels (NEFL, ABO, ZAN) in the transcript 
> relative to GRCh37?
>
> Thanks,
> Reece
>
>
>
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