[ensembl-dev] Gene and RS

[Igo Medeiros]

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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