[ensembl-dev] Gene and RS

[Igo Medeiros]

I am study the documentation about VEP too.


2014-04-16 11:52 GMT-03:00 Igo Medeiros <igo701 at gmail.com>:

> 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
>



-- 
Igo Paixão de Medeiros
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