<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi Joshua</div><div><br></div><div>If you are referring to our ensembl_id field in the object_xref table then it's any one of a number of fields. Ensembl id refers to the primary key from</div><div><br></div><div>- gene</div><div>- transcript</div><div>- translation</div><div>- operon</div><div>- operon_transcript</div><div><br></div><div>The ensembl_object_type indicates the source of the identifier e.g. An object type of Gene means ensembl_id is equivalent to gene_id in the gene table.</div><div><br></div><div>I will urge a lot of caution of using the SQL schema directly. The relations are not the easiest to follow and we can make large changes. However if you want a lot of different types of annotation data linked to the central objects (especially genes and variants) have you taken a look at biomart our data warehouse tool? You can access the tool from <a href="http://www.ensembl.org/biomart">http://www.ensembl.org/biomart</a> and a video from <a href="http://www.ensembl.org/Multi/Help/Movie?db=core;id=189">http://www.ensembl.org/Multi/Help/Movie?db=core;id=189</a></div><div><br></div><div>Hope this helps you get to the data you need quickly</div><div><br></div><div>Best regards</div><div><br></div><div>Andy<br><br>Sent from my mobile.</div><div><br>On 26 May 2014, at 14:20, Joshua Orvis <<a href="mailto:jorvis@gmail.com">jorvis@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Is there any chance you could give an example of an annotation attribute keyed on the ensembl_id? I looked around the schema docs before I wrote this e-mail, specifically for the gene product name, and couldn't find it.<div>
<br></div><div>JO</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 26, 2014 at 1:19 AM, Manuel Alfonso López Rourich <span dir="ltr"><<a href="mailto:alfonso.lopez@cenits.es" target="_blank">alfonso.lopez@cenits.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, <div><br></div><div>Getting annotations for Ensembl IDs it's easy with a Perl script by using the Ensembl Perl API. Have a look at the database schema to see what information you can get for your different types of data through this link <a href="http://www.ensembl.org/info/docs/api/index.html" target="_blank">http://www.ensembl.org/info/docs/api/index.html</a>.</div>
<div><br></div><div>Regards, </div><div><br></div><div><table border="0" cellpadding="0" width="425" style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;margin-left:auto;margin-right:auto"><tbody><tr>
<td colspan="2" valign="top"><div style="text-align:center"><span style="font-size:xx-small"><strong> Manuel Alfonso López Rourich</strong></span></div><div style="text-align:center"><span style="font-size:xx-small"> Técnico de Apoyo</span></div>
<div style="text-align:center"><span style="font-size:xx-small"> <a href="mailto:alfonso.lopez@cenits.es" target="_blank">alfonso.lopez@cenits.es</a></span></div></td></tr><tr><td width="500" valign="top"><div>
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</div></td></tr></tbody></table><div style="font-family:arial,sans-serif;font-size:13px"><p style="text-align:justify"><font face="Tahoma" size="1" color="#000000">En cumplimiento de la Ley Orgánica 15/1999, de 13 de diciembre, de Protección de Datos de Carácter Personal, conforme art. 5 relativo al derecho de la información en la recogida de datos, se le informa de que los datos de carácter personal de los que disponemos, son incorporados en un fichero automatizado propiedad de la Fundación COMPUTAEX, responsable del tratamiento y destinatario de los datos, con domicilio en Carretera Nacional 521, km 41.8, 10071 Cáceres. Podrá ejercitar los derechos de acceso, rectificación, cancelación y oposición dirigiéndose al responsable del fichero a la dirección indicada. </font></p>
</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-05-26 4:15 GMT+02:00 Joshua Orvis <span dir="ltr"><<a href="mailto:jorvis@gmail.com" target="_blank">jorvis@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">I have a list of several thousand ENSEMBL IDs, such as ENSMUSG00000039372, and I want to automate a way to get whatever associated annotation attributes from them that I can, such as gene product name, gene symbol, GO terms, etc. From pages like this I see that I can get at least the product name, labeled as "Description":<div>
<br></div><div><a href="http://uswest.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000039372" target="_blank">http://uswest.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000039372</a><br></div><div>
<br></div><div>For this one, it would be "membrane-associated ring finger (C3HC4) 4". </div>
<div><br></div><div>I tried connecting to the MySQL database but couldn't find where this is stored. What is the best way to get this sort of information for a lot of IDs? MySQL, Perl, Python, whatever solution is fine.</div>
<div><br></div><div>Thanks!</div><span><font color="#888888"><div><br>Joshua</div></font></span></div>
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