<div dir="ltr"><div>Sorry for my <span id="result_box" class="" lang="en"><span class="">lack of attention. I saw the table.<br></span></span></div><span id="result_box" class="" lang="en"><span class="">Thank you for help.<br>
<br></span></span></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-04-16 11:52 GMT-03:00 Igo Medeiros <span dir="ltr"><<a href="mailto:igo701@gmail.com" target="_blank">igo701@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I am study the documentation about VEP too.<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">
2014-04-16 11:52 GMT-03:00 Igo Medeiros <span dir="ltr"><<a href="mailto:igo701@gmail.com" target="_blank">igo701@gmail.com</a>></span>:<div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>How can I access gene table?<br></div>I saw VEP, but i need study more about. <br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2014-04-16 11:16 GMT-03:00 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>:<div><div><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Have you considered using our Variant Effect Predictor tool (VEP)?<div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/index.html" target="_blank">http://www.ensembl.org/info/docs/tools/vep/index.html</a><br>
</div><div><br></div><div>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.</div>
<div><br></div><div>The gene name is found in the xref (external reference) table, linked via the display_xref_id column in the gene table:</div><div><br></div><div>SELECT display_label</div><div>FROM gene g, xref x</div>
<div>WHERE g.display_xref_id = x.xref_id</div><div>AND g.stable_id = '<span style="color:rgb(80,0,80)">ENSG00000196218';</span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 16 April 2014 14:55, Igo Medeiros <span dir="ltr"><<a href="mailto:igo701@gmail.com" target="_blank">igo701@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Thank you,<br></div>
both are help me.<br></div>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.<br>
</div>I am usuing PHP ang JQuery, but I would like to change the project, that i am doing, to Perl and BioJS.<br><br></div>There is a other thing. How can I find for gene name? I am looking for all schema, but until now not found.<br>
<br></div>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.<br><br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2014-04-16 10:02 GMT-03:00 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>:<div><div><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">If you do want a quick way to get all rsIDs that fall in a gene, this query should work:<div><br></div><div><div><div>SELECT vf.variation_name</div><div>FROM homo_sapiens_variation_75_37.variation_feature vf, homo_sapiens_core_75_37.gene g</div>
<div>WHERE g.seq_region_id = vf.seq_region_id</div><div>AND vf.seq_region_end >= g.seq_region_start</div><div>AND vf.seq_region_start <= g.seq_region_end</div><div>AND vf.source_id = 1</div><div>AND g.stable_id = 'ENSG00000196218'</div>
</div><div><br></div><div>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.</div>
<div>
<br></div><div>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.</div></div><div><br></div><div>The REST API is particularly suited to this sort of task; the following URL retrieves all variants in a gene with ID ENSG00000157764:</div>
<div><br></div><div><a href="http://beta.rest.ensembl.org/feature/id/ENSG00000157764?feature=variation;content-type=application/json" target="_blank">http://beta.rest.ensembl.org/feature/id/ENSG00000157764?feature=variation;content-type=application/json</a><br>
</div><div><br></div><div>See <a href="http://beta.rest.ensembl.org/documentation/info/feature_id" target="_blank">http://beta.rest.ensembl.org/documentation/info/feature_id</a> for more details.</div><div><br></div><div>
Regards</div><span><font color="#888888"><div>
<br></div><div>Will McLaren</div><div>Ensembl Variation</div></font></span></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div>On 16 April 2014 13:46, Kieron Taylor <span dir="ltr"><<a href="mailto:ktaylor@ebi.ac.uk" target="_blank">ktaylor@ebi.ac.uk</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div>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.<br>
<br>
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.<br>
<br>
<a href="http://www.ensembl.org/info/docs/api/core/core_schema.html" target="_blank">http://www.ensembl.org/info/<u></u>docs/api/core/core_schema.html</a><br>
<br>
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.<br>
<br>
Regards,<br>
<br>
Kieron Taylor<br>
Ensembl Core</div><div><div><div><br>
<br>
On 16/04/2014 13:17, Igo Medeiros wrote:<br>
</div><div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi,<br>
how can I found relation, in DB, between Gene and all RS inside Gene?<br>
there are columns like seq_region_start, seq_region_end ans<br>
seq_region_id those repeat in three tables(variation_feature,<br>
structural_variation_feature and phenotype_feature), what the diferent<br>
between them?<br>
Sorry for my english, its not so good. And thank you for help.<br>
<br>
--<br>
Igo Paixão de Medeiros<br>
<br>
</blockquote>
<br>
<br></div></div></div></div><div>
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<br></blockquote></div></div></div><div><div><br><br clear="all"><br>-- <br>Igo Paixão de Medeiros
</div></div></div>
</blockquote></div></div></div><div><div class="h5"><br><br clear="all"><br>-- <br>Igo Paixão de Medeiros
</div></div></div>
</blockquote></div><br><br clear="all"><br>-- <br>Igo Paixão de Medeiros
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