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

[Andy Yates]

Hi Joshua

If you are referring to our ensembl_id field in the object_xref table then it's any one of a number of fields. Ensembl id refers to the primary key from

- gene
- transcript
- translation
- operon
- operon_transcript

The ensembl_object_type indicates the source of the identifier e.g. An object type of Gene means ensembl_id is equivalent to gene_id in the gene table.

I will urge a lot of caution of using the SQL schema directly. The relations are not the easiest to follow and we can make large changes. However if you want a lot of different types of annotation data linked to the central objects (especially genes and variants) have you taken a look at biomart our data warehouse tool? You can access the tool from http://www.ensembl.org/biomart and a video from http://www.ensembl.org/Multi/Help/Movie?db=core;id=189

Hope this helps you get to the data you need quickly

Best regards

Andy

Sent from my mobile.

> On 26 May 2014, at 14:20, Joshua Orvis <jorvis at gmail.com> wrote:
> 
> 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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