<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>
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</pre>
    </blockquote>
    <pre cols="72"></pre>
  </div>

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