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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It might be worth advertising here that we are still maintaining our Java Ensembl API.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">JEnsembl can be used to load & access all releases of Ensembl and EnsemblGenomes (back to Ensembl release 50).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">For the non-bacterial datasources full backwards compatibility is provided and multiple releases can be loaded and traversed by the API.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Because the Bacterial species list is now so large we have restricted the API Registry to working with a single bacterial release at a time .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The JEnsembl API can be found at
<a href="http://jensembl.sourceforge.net/">http://jensembl.sourceforge.net/</a> .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">ArkMAP, our demonstration Map drawing application (<a href="http://bioinformatics.roslin.ed.ac.uk/arkmap/">http://bioinformatics.roslin.ed.ac.uk/arkmap/</a>),
can be used to pull down and draw chromosomes from any of the Ensembl datasources and retrieve and align homology relationships between genomes.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">We intend to keep the API and ArkMAP up-do-date with Ensembl releases – but are not *<b>currently</b>* implementing additional functionality.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">(although we would consider interesting use cases, particularly those that have potential to turn into funded collaborations).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Trevor Paterson PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><a href="mailto:trevor.paterson@roslin.ed.ac.uk">trevor.paterson@roslin.ed.ac.uk</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Bioinformatics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">The Roslin Institute<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Royal (Dick) School of Veterinary Studies
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">University of Edinburgh
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Easter Bush<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Midlothian<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">EH25 9RG<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Scotland UK<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">phone +44 (0)131 651 9157<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><a href="http://bioinformatics.roslin.ed.ac.uk/">http://bioinformatics.roslin.ed.ac.uk/</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland
with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Beat Wolf<br>
<b>Sent:</b> 24 February 2015 10:14<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Bacteria Biomart<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">Hi,<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">following the question about the biomart access to Ensembl bacteria/genomes i
<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">got interested in the data myself. I quickly found that there is a REST API to access
<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">the data, which is great. But sadly it does not seem to work correctly. Most of the
<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">examples gives in the API description do not work and i got a lot of issues. Simple
<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">requests like retrieving the list of supported species
<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;-qt-block-indent:0;-qt-user-state:0">
<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">(<a href="http://rest.ensemblgenomes.org/documentation/info/species%5b1">http://rest.ensemblgenomes.org/documentation/info/species[1</a>] ) give an error.<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">Is this known? Is there a plan in improving that rest interface and a timetable? Or is
<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;-qt-block-indent:0;-qt-user-state:0">
<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">the API documentation simply out of date and the REST interface actually works
<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">but has different endpoints than described?<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">Thank you for your help<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;-qt-block-indent:0;-qt-user-state:0">
<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">Kind regards<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">Beat Wolf<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">On Monday 23 February 2015 17.03:47 Dan Staines wrote:<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> Hi Toni,<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> We no longer provide a BioMart for Ensembl Bacteria following its<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> expansion to over 20,000 genomes, which BioMart does not scale to. We're<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> actively looking into alternative tools to replace mart - in the<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> meantime, if you have specific needs, I'd be more than happy to help as<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> far as I can.<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> Regards,<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">> Dan.<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""><br>
-- <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">-----------------------------------------------------------------------<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">PhD Student Beat Wolf<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">University of Applied Sciences of Western Switzerland<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">&<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">University of Würzburg<o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif""> <o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Ubuntu","serif"">PhD Website: <a href="http://beat.wolf.home.hefr.ch/">
<span style="color:#0057AE">http://beat.wolf.home.hefr.ch/</span></a> <o:p></o:p></span></p>
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