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Issue #2681 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15405?detail_id=1757">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Migrated</i></li>
</ul>
<p>Migrated to GitHub issue <a class="external" href="https://github.com/biopython/biopython/issues/1718">https://github.com/biopython/biopython/issues/1718</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2681#change-15405">Bug #2681: BioSQL: record annotations enhancements</a></h1>
<ul><li>Author: Cymon J.</li>
<li>Status: Migrated</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: BioSQL</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>BioSQL storage and retrieval of record annotations. See also bug 2396.</p>
<p>Patch fixes 3 annotations:</p>
<p>1) Fixed date/dates typo.<br />2) comment's were being stored by not retrieved - fixed with test.<br />3) A 'reference' annotation, even if an empty list, was being retrieved in a<br />DBSeqRecord. Fixed so that if there are no references there is no annotation in<br />DBSeqRecord.</p>
<p>Other annotations:</p>
<p>'date', 'ncbi_taxid', 'gi', and 'contig' are the only annotations we are not<br />handling correctly in the test suite.</p>
<p>'date' can be ignored if present in DBSeqRecord but absent in SeqRecord because the current date is entered into table if a date is not present in the record.</p>
<p>Annotation 'ncbi_taxid' will be present in the DBSeqRecords even when not<br />present in the loaded SeqRecord as they are grabbed from the taxon table. We can<br />therefore ignore this specific comparision: old record absent, new record<br />present. Some swiss prot SeqRecords have ncbi_taxid and they are retrieved correctly by DBSeqRecord. TODO: others have ncbi_taxid that is missing from the retrieved DBSeqRecord: sp012, sp014,</p>
<p>Swissprot, fasta, and EMBL SeqRecords dont have a gi annotation, retrieved<br />DBSeqRecords do. Loader uses the 'record_id' (line 522) as the identifier in<br />bioentry, if the gi annotation is missing, which is pulled as the gi annotation.<br />So the swissprot, fasta, and embl DBSeqRecords return the accession as the gi<br />(GenBank identifier). I think this is misleading; annotation 'gi' in the<br />DBSeqRecord should really be named a more generic 'identifier'... What to do<br />here?</p>
<p>'contig' is ignored by loader because it's a SeqFeature object. Is there any reason it couldnt be loaded and retrieved? (record is GenBank/NT_019265.gb)</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1074/annotations1.patch">annotations1.patch</a>
(3.9 KB)<br />
</fieldset>
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