<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi Ramiro</p>
<p>Correct: the archive/id endpoint doesn't know how to retrieve the
history of gene-tree and family IDs</p>
<p>Matthieu<br>
</p>
<div class="moz-cite-prefix">On 31/07/2019 16:34, Ramiro Magno
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20190731153738.6DA1C62CF24_D41B5C2B@hh-mx3.ebi.ac.uk">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Thibaut,<br>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>So, although all entities are the ones listed in e.g., <a
href="https://www.ensembl.org/info/genome/stable_ids/prefixes.html"
moz-do-not-send="true">https://www.ensembl.org/info/genome/stable_ids/prefixes.html</a>,
the ones that are retrievable via the endpoint "GET
archive/id/:id" are only: gene, transcript, protein and exon.
Correct?</div>
<div><br>
</div>
<div>For example, if I try to get a gene tree, e.g.
ENSGT00390000013823: <a
href="https://rest.ensembl.org/archive/id/ENSGT00390000013823?content-type=application/json"
moz-do-not-send="true">https://rest.ensembl.org/archive/id/ENSGT00390000013823?content-type=application/json</a></div>
<div><br>
</div>
<div>the server replies with "<span style="color:rgb(0,0,0);white-space:pre-wrap">{"error":"No object found for ENSGT00390000013823"}</span>".</div>
<div><br>
</div>
<div>Cheers, RM</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, 31 Jul 2019 at 11:20,
Thibaut Hourlier <<a href="mailto:thibaut@ebi.ac.uk"
moz-do-not-send="true">thibaut@ebi.ac.uk</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
Ramiro<br>
<br>
Ensembl ID and stable id are the same id. We will have a look
at how we can rephrase the two documents to try to remove the
ambiguity.<br>
<br>
The list of entities is correct in the FAQ and <a
href="https://www.ensembl.org/info/genome/stable_ids/prefixes.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/genome/stable_ids/prefixes.html</a>.
The document <a
href="https://www.ensembl.org/info/genome/stable_ids/index.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/genome/stable_ids/index.html</a>
refers to the stable ids and versioning of genes, transcripts,
proteins and exons, this is why they do not have all the
entities.<br>
<br>
Thanks<br>
Thibaut<br>
<br>
> On 30 Jul 2019, at 16:02, Ramiro Magno <<a
href="mailto:ramiro.magno@gmail.com" target="_blank"
moz-do-not-send="true">ramiro.magno@gmail.com</a>> wrote:<br>
> <br>
> Hi Devs,<br>
> <br>
> I have two questions about Ensembl identifiers:<br>
> <br>
> (i) Ensembl ID and Stable identifiers are the same
concept?<br>
> <a href="https://www.ensembl.org/Help/Faq?id=488"
rel="noreferrer" target="_blank" moz-do-not-send="true">https://www.ensembl.org/Help/Faq?id=488</a><br>
> <a
href="https://www.ensembl.org/info/genome/stable_ids/index.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/genome/stable_ids/index.html</a><br>
> <br>
> In one case the version suffix seems to be purposefully
left out, so I am not sure if by stable you mean without the
id version suffix, and whether you reserve the general
expression "Ensembl ID" for the five part identifier.<br>
> <br>
> (ii) What are the entity types referred by these IDs? Is
it just the four entities (gene, transcript, protein and exon)
as described here <a
href="https://www.ensembl.org/info/genome/stable_ids/index.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/genome/stable_ids/index.html</a>
or are there more entities as hinted here <a
href="https://www.ensembl.org/Help/Faq?id=488"
rel="noreferrer" target="_blank" moz-do-not-send="true">https://www.ensembl.org/Help/Faq?id=488</a>
(e.g., FM, protein family, R, regulatory feature and GT, gene
tree)? <br>
> <br>
> Many thanks!<br>
> <br>
> Ramiro</blockquote>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room A3-123
Phone + 44 (0) 1223 49 4631
Fax + 44 (0) 1223 49 4468</pre>
</body>
</html>