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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>We are using 4store and, so far are quite happy with it. At the moment we are spending all our time fixing some stuff that we have, knowingly or unknowingly, broken.<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'>Ray<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><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='margin-left:.5in'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Lee Watkins [mailto:lee.watkins@jhmi.edu] <br><b>Sent:</b> Wednesday, October 02, 2013 2:24 PM<br><b>To:</b> Ray Fergerson<br><b>Cc:</b> support@bioontology.org<br><b>Subject:</b> Re: [bioontology-support] New triple-store backend<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in'><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'>Thanks!  So what triplestore are you using now?  TDB or something like SparkleDB or maybe a graph database?  How you reparsed the ontology files may have decided that for you, I guess.  Since this is fairly esosteric knowledge and something very few people have actually done, a technical report on it would be very informative to people like me who are trying to come to grips with this whole domain.  Not that you need more work to do, I’m sure...Lee<br><br><br>On 10/2/13 4:46 PM, "Ray Fergerson" <<a href="ray.fergerson@stanford.edu">ray.fergerson@stanford.edu</a>> wrote:</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in'><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'>Previously we stored data in Protégé 3 database format and the LexEVS database format. These were migrated to a triple store by reparsing the original ontology files (we didn’t try to migrate the previous formats). We were driven to make this change because we wanted a uniform way to store things and wanted to be able to provide a SPARQL based access to the underlying ontologies and metadata.<br> <br>Ray<br> <br><br></span><b><span style='font-size:10.0pt;font-family:"Lucida Grande","serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Lucida Grande","serif"'> <a href="bioontology-support-bounces@lists.stanford.edu">bioontology-support-bounces@lists.stanford.edu</a> [<a href="mailto:bioontology-support-bounces@lists.stanford.edu">mailto:bioontology-support-bounces@lists.stanford.edu</a>] <b>On Behalf Of </b>Lee Watkins<br><b>Sent:</b> Tuesday, October 01, 2013 11:13 AM<br><b>To:</b> <a href="support@bioontology.org">support@bioontology.org</a><br><b>Subject:</b> [bioontology-support] New triple-store backend<br></span><br><span style='font-family:"Lucida Grande","serif"'>I'm interested to know what you used for your "</span>new triple-store backend storage system<span style='font-family:"Lucida Grande","serif"'>" and what was involved in migrating from triples stored in a relational database (which is what I'm guessing you used previously?), and what drove you to make the change.<br>Thanks,<br>Lee<br></span><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span><br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>--- <br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>Lee Watkins, Jr.<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>Director of Bioinformatics & IT<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>Center for Inherited Disease Research<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>McKusick-Nathans Institute of Genetic Medicine<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>Johns Hopkins University School of Medicine<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>333 Cassell Drive, Triad 2000<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>Baltimore, MD 21224<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span><br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span>410-550-6702 w | 410-903-2989 c [urgent_only]<br><span style='font-size:11.0pt;font-family:"Lucida Grande","serif"'><br></span><a href="lee.watkins@jhmi.edu">lee.watkins@jhmi.edu</a> | <a href="http://www.cidr.jhmi.edu">http://www.cidr.jhmi.edu</a><o:p></o:p></p></div></body></html>