[ensembl-dev] Gene and RS

[Igo Medeiros]

How can I access gene table?
I saw VEP, but i need study more about.


2014-04-16 11:16 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:

> 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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>>
>>
>
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-- 
Igo Paixão de Medeiros
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