[ensembl-dev] Gene and RS

[Will McLaren]

Have you considered using our Variant Effect Predictor tool (VEP)?

http://www.ensembl.org/info/docs/tools/vep/index.html

It's very useful for investigating novel variations found in sequencing
experiments and the like, and can probably give you a lot of the
information you need without having to write any code.

The gene name is found in the xref (external reference) table, linked via
the display_xref_id column in the gene table:

SELECT display_label
FROM gene g, xref x
WHERE g.display_xref_id = x.xref_id
AND g.stable_id = 'ENSG00000196218';


On 16 April 2014 14:55, Igo Medeiros <igo701 at gmail.com> wrote:

> Thank you,
> both are help me.
> I was looking just in schema homo_sapiens_variation_75_37, not in
> homo_sapiens_core_75_37 too. Now I understand better why a lot of bases.
> I am usuing PHP ang JQuery, but I would like to change the project, that i
> am doing, to Perl and BioJS.
>
> There is a other thing. How can I find for gene name? I am looking for all
> schema, but until now not found.
>
> All this is because If don't exist the variation found in lab, in UFPA, in
> the schemas, I have to find all things connected with that area of
> sequence. And publications.
>
>
>
> 2014-04-16 10:02 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:
>
> If you do want a quick way to get all rsIDs that fall in a gene, this
>> query should work:
>>
>> SELECT vf.variation_name
>> FROM homo_sapiens_variation_75_37.variation_feature vf,
>> homo_sapiens_core_75_37.gene g
>> WHERE g.seq_region_id = vf.seq_region_id
>> AND vf.seq_region_end >= g.seq_region_start
>> AND vf.seq_region_start <= g.seq_region_end
>> AND vf.source_id = 1
>> AND g.stable_id = 'ENSG00000196218'
>>
>> Replace ENSG00000196218 with the stable identifier of your gene of
>> interest. Remove "AND vf.source_id = 1" if you also want variation features
>> from sources that aren't dbSNP.
>>
>> As Kieron says, we would encourage you to use our perl API, REST API or
>> BioMart, all of which can accomplish this same task without the risks of
>> schema changes.
>>
>> The REST API is particularly suited to this sort of task; the following
>> URL retrieves all variants in a gene with ID ENSG00000157764:
>>
>>
>> http://beta.rest.ensembl.org/feature/id/ENSG00000157764?feature=variation;content-type=application/json
>>
>> See http://beta.rest.ensembl.org/documentation/info/feature_id for more
>> details.
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>>
>> On 16 April 2014 13:46, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:
>>
>>> Ensembl has a table for each genetic feature type, hence we have a
>>> Transcript table, a Gene table, and one for each class of variation. Each
>>> table shares a common set of fields, plus more that are specific to that
>>> feature. This is slightly contrary to a traditionally normalised schema.
>>>
>>> It is not clear to me what you mean by "RS inside a Gene". If you wish
>>> to understand our schema, please take a look at the following link.
>>>
>>> http://www.ensembl.org/info/docs/api/core/core_schema.html
>>>
>>> I urge you to find another way to access our data if at all possible.
>>> Direct SQL queries against our schema is sometimes the right solution, but
>>> suffers when we have to make changes in later releases. Our API and other
>>> services insulate you from these changes. Also, some commonly required data
>>> is computed and therefore cannot be found in the database at all.
>>>
>>> Regards,
>>>
>>> Kieron Taylor
>>> Ensembl Core
>>>
>>>
>>> On 16/04/2014 13:17, Igo Medeiros wrote:
>>>
>>>> Hi,
>>>> how can I found relation, in DB, between Gene and all RS inside Gene?
>>>> there are columns like seq_region_start, seq_region_end ans
>>>> seq_region_id those repeat in three tables(variation_feature,
>>>> structural_variation_feature and phenotype_feature), what the diferent
>>>> between them?
>>>> Sorry for my english, its not so good. And thank you for help.
>>>>
>>>> --
>>>> Igo Paixão de Medeiros
>>>>
>>>>
>>>
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>>
>>
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>>
>
>
> --
> Igo Paixão de Medeiros
>
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