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Issue #3156 has been updated by Vincent Davis.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15358?detail_id=1650">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Closed</i></li>
<li><strong>Assignee</strong> changed from <i>Biopython Dev Mailing List</i> to <i>Vincent Davis</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>working as designed/intended. Closing</p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/3156#change-15358">Bug #3156: UniProt XML and SwissProt parsers silently fail to parse all of database references</a></h1>
<ul><li>Author: Renato Alves</li>
<li>Status: Closed</li>
<li>Priority: Normal</li>
<li>Assignee: Vincent Davis</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>Example code:</p>
<p>from Bio import SeqIO, ExPASy<br />entry = SeqIO.read(ExPASy.get_sprot_raw('P31946'), 'swiss')</p>
<p>If you then inspect entry.dbxrefs, you can see that it includes:</p>
<p>['Ensembl:ENST00000353703', 'Ensembl:ENST00000372839']</p>
<p>but not<br />['Ensembl:ENSP00000300161', 'Ensembl:ENSG00000166913'. 'Ensembl:ENSP00000361930', 'Ensembl:ENSG00000166913']</p>
<p>which are present in the original file as:<br />DR Ensembl; ENST00000353703; ENSP00000300161; ENSG00000166913.<br />DR Ensembl; ENST00000372839; ENSP00000361930; ENSG00000166913.</p>
<p>The same happens with the XML format and the new uniprot-xml parser where the original file contains:</p>
<p><dbReference type="Ensembl" id="ENST00000353703" key="75"><br /><property type="protein sequence ID" value="ENSP00000300161" /><br /><property type="gene ID" value="ENSG00000166913" /><br /></dbReference></p>
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