[ensembl-dev] Gene and RS

Thu Apr 17 13:02:34 BST 2014

Is there a table in some base that have information about disease?

2014-04-16 12:10 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:

> 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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>>
>>
>
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>

-- 
Igo Paixão de Medeiros
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