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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Recently the module Bio.EBI.dbfetch has been reviewed and made ready for merging into the master branch.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The module is restricted to the ‘dbfetch’ service only.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Few days ago Peter found out a script that can deal with the entire EBI Search API:
<a href="https://github.com/bebatut/ebisearch"><span style="color:#0563C1">https://github.com/bebatut/ebisearch</span></a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This script goes way beyond dbfetch only and provide access to the EBI Search API in full, which in turn provide access to the following repositories:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">European Nucleotide Archive (ENA)<o:p></o:p></p>
<p class="MsoNormal">Ensembl Genomes<o:p></o:p></p>
<p class="MsoNormal">RNAcentral<o:p></o:p></p>
<p class="MsoNormal">InterPro<o:p></o:p></p>
<p class="MsoNormal">dbfetch/WSDbfetch<o:p></o:p></p>
<p class="MsoNormal">MetaboLights<o:p></o:p></p>
<p class="MsoNormal">Enzyme portal<o:p></o:p></p>
<p class="MsoNormal">Expression Atlas<o:p></o:p></p>
<p class="MsoNormal">Gene & protein summaries<o:p></o:p></p>
<p class="MsoNormal">PomBase<o:p></o:p></p>
<p class="MsoNormal">Job Dispatcher<o:p></o:p></p>
<p class="MsoNormal">HMMER<o:p></o:p></p>
<p class="MsoNormal">LRG<o:p></o:p></p>
<p class="MsoNormal">EMBOSS<o:p></o:p></p>
<p class="MsoNormal">Omics Discovery Index<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">More info here: <a href="http://www.ebi.ac.uk/ebisearch/overview.ebi">
<span style="color:#0563C1">http://www.ebi.ac.uk/ebisearch/overview.ebi</span></a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I would like to know if people are interested in any of the following options:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoNormal" style="margin-left:0cm;mso-list:l0 level1 lfo1">Ignore the scripts and merge the Bio.EBI.dbfetch module to the Biopython master<o:p></o:p></li><li class="MsoNormal" style="margin-left:0cm;mso-list:l0 level1 lfo1">Contact the developer for this script and incorporate it into Biopython<o:p></o:p></li></ul>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The licence term for this script is pretty relaxed ( <a href="https://github.com/bebatut/ebisearch/blob/master/LICENSE">
<span style="color:#0563C1">https://github.com/bebatut/ebisearch/blob/master/LICENSE</span></a> ) but extending a request for collaboration before hand is in order.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any thoughts?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,<o:p></o:p></p>
<p class="MsoNormal">Francesco<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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