[BioC] Marts downloads

[steffen at stat.Berkeley.EDU]

Hi Amanda,

To know if the aceview information is available in Ensembl I would contact
the Ensembl helpdesk at helpdesk at ensembl.org

For a local Ensembl installation and queries with biomaRt:
You can find the tables for a local Mart installation here:

ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_50/

You can create the ensembl_mart_50 tables with the sql script from:

ensembl_mart_50.sql.gz

For the human dataset you'll definitely need the data from the files below
to fill the tables with the same table names (omitting .txt.gz):

hsapiens_gene_ensembl__gene__main.txt.gz
meta_conf__dataset__main.txt.gz
meta_conf__xml__dm.txt.gz

Depending on which queries you want to make, you'll need additional
hsapiens tables.

Cheers,
Steffen

>
> Is there a mart for aceview available for GenomeGraphs? I'm looking to be
> able to query using aceview varient names. And when installing a local
> version of the ensembl_mart_50, where would I find the .sql file and the
> tables meta_conf__dataset__main.txt.table
> meta_conf__xml__dm.txt.table.?
>
> Thank you.
>
>
>
> Amanda Miotto
> a.miotto at griffith.edu.au
>
> Software Engineer.
> Research Computing Services
> INFORMATION SERVICES
> Griffith University, NATHAN 4111, AUSTRALIA
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