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

Manuel Alfonso López Rourich alfonso.lopez at cenits.es
Mon May 26 07:19:26 BST 2014


Hi,

Getting annotations for Ensembl IDs it's easy with a Perl script by using
the Ensembl Perl API. Have a look at the database schema  to see what
information you can get for your different types of data through this link
http://www.ensembl.org/info/docs/api/index.html.

Regards,

*           Manuel Alfonso López Rourich*
          Técnico de Apoyo
            alfonso.lopez at cenits.es


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2014-05-26 4:15 GMT+02:00 Joshua Orvis <jorvis at gmail.com>:

> 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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