(Where) can I download the Ensembl cross reference database?
1
0
Entering edit mode
8.1 years ago

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 • 2.5k views
ADD COMMENT
3
Entering edit mode
8.1 years ago
Emily 23k

That would be the Perl API

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 856 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6