[ensembl-dev] Getting primary annotation data via the API

Joshua Orvis jorvis at gmail.com
Mon May 26 03:15:15 BST 2014


I have a list of several thousand ENSEMBL IDs, such as ENSMUSG00000039372,
and I want to automate a way to get whatever associated annotation
attributes from them that I can, such as gene product name, gene symbol, GO
terms, etc.  From pages like this I see that I can get at least the product
name, labeled as "Description":

http://uswest.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000039372

For this one, it would be "membrane-associated ring finger (C3HC4) 4".

I tried connecting to the MySQL database but couldn't find where this is
stored.  What is the best way to get this sort of information for a lot of
IDs?  MySQL, Perl, Python, whatever solution is fine.

Thanks!

Joshua
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