[ensembl-dev] loading NCBI exon structures into Ensembl

Reece Hart reece at harts.net
Thu Jun 2 18:05:39 BST 2011


On Wed, Jun 1, 2011 at 1:39 AM, Bronwen Aken <ba1 at sanger.ac.uk> wrote:

> For the RefSeq models, RefSeq provides us with a flat file giving the
> genomic coordinates for all genes, transcripts and exons in their gene set.
> We load this up directly into the otherfeatures database and do not change
> any coordinates.
>

Hi Bronwen-

Does NCBI provide this to you directly, or is it buried in a ftp directory
somewhere? Getting this data via eutils is slow and convoluted, so I'd be
thrilled to have a simpler route.

In v62 otherfeatures, meta shows the xref.timestamp as '2010-06-22
23:25:07'. Do I correctly infer that the otherfeatures data are about a year
old?

I would love to be able to recreate exactly what Ensembl does for
otherfeatures, but with newer data. Are there scripts and/or documentation
somewhere?

Thanks,
Reece
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