(Where) can I download the Ensembl cross reference database?

Question

[samuel.lampa]

Ensembl has released a beta of a great new REST API for converting between different gene identifiers, over at:

http://beta.rest.ensembl.org/documentation/info/xref_id

We need to do some heavy parsing of some gene ids though, and thought it might be better to download a dump of this data locally rather than sinking the REST endpoint.

Anybody knows if - and if so, where - I can do that?

Answer 1

[Emily]

That would be the Perl API

[samuel.lampa]

Thanks, that was quick! :) I'm now studying http://www.ensembl.org/info/docs/api/api_installation.html ... Would be cool if there was one big json-dump of the xrefs data though, but I guess with a little work I can get the perl API up and running too.

[Emily]

There's so much data that it's all stored in MySQL tables.