<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Dear Hao Luo,<br>
<br>
There is an endpoint to list available external_db names for a
species, so you don't have to remember our jargon (*)<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/documentation/info/external_dbs">http://rest.ensembl.org/documentation/info/external_dbs</a><br>
It is also possible to filter it using wildcards, something like<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/info/external_dbs/homo_sapiens?content-type=text/xml;filter=Uniprot%">http://rest.ensembl.org/info/external_dbs/homo_sapiens?content-type=text/xml;filter=Uniprot%</a><br>
<br>
It is also possible to use wildcard on the xref endpoint, removing
the need to know exact UniProt syntax<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/xrefs/id/ENST00000288602?content-type=application/json;external_db=uniprot%;all_levels=1">http://rest.ensembl.org/xrefs/id/ENST00000288602?content-type=application/json;external_db=uniprot%;all_levels=1</a><br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
* Some background on the jargon<br>
Historically, we have distinguished between Swissprot/curated
UniProt entries (UniProt/SWISSPROT) and Trembl/predicted UniProt
(UniProt/TREMBL) entries.<br>
These are protein entries, so will be mapped to our Ensembl
translations.<br>
Uniprot_gn is our internal way of naming gene symbols obtained via
UniProt protein mappings.<br>
These are mapped to the Ensembl genes, so will not be returned with
the all_levels option on a transcript, as this only returns xrefs
for the transcript and its translation, not the gene.<br>
<br>
<div class="moz-cite-prefix">On 02/12/2015 09:57, Luo Hao wrote:<br>
</div>
<blockquote
cite="mid:AMUAIAATAAInsxIJ2MmsRqp7.1.1449050244574.Hmail.3007210045@tju.edu.cn"
type="cite">
<div>Dear all,</div>
<div>I have a list of ensemble id and want to get Uniprot ID by
ENSEMBL ID with ENSEMBL REST API, and use <span
style="line-height: 1.5;">python ensemblrest module.</span></div>
<div><br>
</div>
<div>But when I used xrefs/id/:id/ apt, I am not clear short name
of external_db parameter for uniprot.</div>
<div>For example, the url for uniprot gene name is
ok, <a class="moz-txt-link-freetext" href="http://rest.ensembl.org/xrefs/id/ENSG00000135334?content-type=application/json;external_db=uniprot_gn">http://rest.ensembl.org/xrefs/id/ENSG00000135334?content-type=application/json;external_db=uniprot_gn</a>.</div>
<div>But the result of the url of
<a class="moz-txt-link-rfc2396E" href="http://rest.ensembl.org/xrefs/id/ENST00000288602?content-type=application/json;external_db=uniprot;all_levels=1">"http://rest.ensembl.org/xrefs/id/ENST00000288602?content-type=application/json;external_db=uniprot;all_levels=1"</a>
is None.</div>
<div><br>
</div>
<div>
<div>---------------------------------------------------------------------</div>
<div>The code of ensenblrest module</div>
<div>from ensemblrest import EnsemblRest</div>
<div>ensRest = EnsemblRest()</div>
<div>ensRest.getXrefsById(id = '<span style="line-height: 1.5;">ENSG00000135334'</span><span
style="line-height: 1.5;">, external_db = 'uniprot',
all_levels=1)</span></div>
<div>---------------------------------------------------------------------</div>
</div>
<div><br>
</div>
<div>Could someone tell me the short names of external_db
parameters or send me a more detail instruction for REST APT?</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
<div>Hao Luo</div>
<div>
<p class="MsoNormal" style="font-family: Arial, Verdana,
sans-serif; text-align: justify;"><span style="color: rgb(31,
73, 125); font-family: Calibri, sans-serif; font-size:
10.5pt; line-height: 1.5;">Tianjin University</span></p>
<p class="MsoNormal" style="font-family: Arial, Verdana,
sans-serif; text-align: justify;"><span style="font-size:
10.5pt; font-family: Calibri, sans-serif; color: rgb(31, 73,
125);">Tianjin, </span><span style="color: rgb(31, 73, 125);
font-family: Calibri, sans-serif; font-size: 10.5pt;
line-height: 1.5;">China</span></p>
<p class="MsoNormal" style="font-family: Arial, Verdana,
sans-serif; text-align: justify;"><span style="font-size:
10.5pt; font-family: Calibri, sans-serif; color: rgb(31, 73,
125);">Email: <span style="color: blue;"><a
moz-do-not-send="true"
href="http://mail.tju.edu.cn/jy3/compose/main.jsp?sid=808A-7f8l614-4f74l3lvgwwIGigIl2e&to=hluo%40tju.edu.cn"
target="_parent"><a class="moz-txt-link-abbreviated" href="mailto:hluo@tju.edu.cn">hluo@tju.edu.cn</a></a></span></span></p>
<p class="MsoNormal" style="font-family: Arial, Verdana,
sans-serif;"><span style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></p>
</div>
<br>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>