<div dir="ltr">Hi Helen,<br><div><br></div><div>thank you for the information.</div><div><br></div><div>All the best,</div><div><br></div><div>Ramiro</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, 2 Jan 2020 at 16:13, Helen Schuilenburg <<a href="mailto:helens@ebi.ac.uk">helens@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">
<div>
<p>Hi</p>
<p>The REST endpoint
(<a href="https://rest.ensembl.org/documentation/info/variation_consequence_types" target="_blank">https://rest.ensembl.org/documentation/info/variation_consequence_types</a>)
<br>
</p>
<p>and <br>
</p>
<p>the calculated consequences on (
<a href="https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html" target="_blank">https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html</a>)
should return the same values. <br>
</p>
<p>Thank you for for flagging the difference.<br>
<br>
The consequence SO:0001060 sequence_variant will be removed from
the REST endpoint in a future release.<br>
The consequence SO:0001628 intergenic_variant will be used
instead.</p>
<p>The three fields (SO_term, label, description) contain different
information on the consequence type and are used for different
purposes.<br>
<br>
SO_term - Sequence Ontology term for the consequence type<br>
label - A short description of the consequence type used in
labels<br>
description - A freetext description of the consequence type<br>
<br>
For example:<br>
SO_accession: SO:0001822<br>
SO_term: inframe_deletion<br>
description: An inframe non synonymous variant that deletes bases
from the coding sequence<br>
label: inframe deletion<br>
<br>
Regards<br>
Helen<br>
<br>
</p>
<p><br>
</p>
<div>On 27/12/2019 20:50, Ramiro Magno
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Devs,<br>
<div><br>
</div>
<div>BTW: Still about the same endpoint, the output returns four
variables: SO_accession, SO_term, label and description. It
seems the actual values for the last three variables
(SO_term, label and description) always report the same
information. Is that right? Why so?</div>
<div><br>
</div>
<div>Cheers, RM</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, 27 Dec 2019 at 20:42,
Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com" target="_blank">ramiro.magno@gmail.com</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">
<div dir="ltr">Hi Devs,<br>
<div><br>
</div>
<div>This endpoint: <a href="https://rest.ensembl.org/documentation/info/variation_consequence_types" target="_blank">https://rest.ensembl.org/documentation/info/variation_consequence_types</a></div>
<div><br>
</div>
<div>returns one more consequence type than those listed
here: <a href="https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html" target="_blank">https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html</a></div>
<div><br>
</div>
<div>The extra consequence type is the <i>sequence variant</i>
(SO:0001060).</div>
<div><br>
</div>
<div>Is this intended?</div>
<div><br>
</div>
<div>All the best,</div>
<div><br>
</div>
<div>Ramiro Magno</div>
</div>
</blockquote>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<pre cols="72"></pre>
</div>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" rel="noreferrer" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div>