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

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?

database identifier ensembl

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updated 12.3 years ago by Emily

• written 12.3 years ago by samuel.lampa •

1 answer

That would be the Perl API

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written 12.3 years ago by Emily

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.

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updated 6.6 years ago by Ram

• written 12.3 years ago by samuel.lampa •

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

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written 12.3 years ago by Emily

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