[ensembl-dev] Gene and RS

Wed Apr 16 16:10:05 BST 2014

The gene table is in the core database (homo_sapiens_core_75_37):

SELECT x.display_label
FROM homo_sapiens_core_75_37.gene g, homo_sapiens_core_75_37.xref x
WHERE g.display_xref_id = x.xref_id
AND g.stable_id = 'ENSG00000196218';

On 16 April 2014 15:52, Igo Medeiros <igo701 at gmail.com> wrote:

> 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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