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

[Joshua Orvis]

Is there any chance you could give an example of an annotation attribute
keyed on the ensembl_id?  I looked around the schema docs before I wrote
this e-mail, specifically for the gene product name, and couldn't find it.

JO


On Mon, May 26, 2014 at 1:19 AM, Manuel Alfonso López Rourich <
alfonso.lopez at cenits.es> wrote:

> 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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>>
>
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