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<p class="MsoNormal">Thank you, John for the response. <o:p></o:p></p>
<p class="MsoNormal">I will contact Agroportal regarding the sparql endpoint. For my problem with loading SNOMED, I am using the same process (umls2rdf) that I use to generate other UMLS terminologies (like RxNomr, LOINC, ICDx, etc.), per Bioportal instruction.
 The default output of umls2rdf script is ttl (load on code). ICD9/10, RxNomr, and LOINC ttl files were successfully loaded and parsed in Bioportal though.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks again for looking into this <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sina  <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">John Graybeal <jgraybeal@stanford.edu><br>
<b>Date: </b>Friday, February 2, 2018 at 2:28 AM<br>
<b>To: </b>"Madani, Sina" <Sina.Madani@vumc.org><br>
<b>Cc: </b>"support@bioontology.org" <support@bioontology.org><br>
<b>Subject: </b>Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody">Hi Sina, <o:p></o:p></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Yes, the 4store backend essentially is a sparql endpoint, used by the rest of the Virtual Appliance. But it could be configured to be accessed also by other query originators. I suggest you contact
 the Agroportal folks to learn about their process and experience. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I think we haven't managed to answer your question, though I may have missed it. (We are a little time-constrained this week, sorry!)  <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">But at a quick guess (only partially informed, apologies in advance if I get something wrong here), I would not expect loading the TTL file to work that way, and I would not expect the size to
 be an issue, since we've loaded big ontologies a lot without an issue related to their size. Naively perhaps, I would consider converting your ontologies of interest to OWL and loading them through the normal process, unless you want to execute the whole UMLS
 load software (not recommended, very complex!).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I think we'll be able to come back to you with more thoughts soon, hopefully by the weekend.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">John<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">On Feb 1, 2018, at 11:51 AM, Madani, Sina <</span><a href="mailto:Sina.Madani@vumc.org"><span style="mso-bookmark:_MailOriginalBody">Sina.Madani@vumc.org</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">>
 wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D">Hi John,</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D"> </span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D">Thank you for getting back to me. Yes, I meant similar functionality like the sparql end point at the Stanford instance.</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D">I understand that many (if not all) of the queries perhaps can be done via APIs but I was just curious to see if the appliance can be configured as an sparql end point
 for incoming sparql queries, like for extracting and validating the mappings that is done automatically by the appliance or regular queries.   </span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D">We are evaluating your appliance for search/browse and visualization purposes for our order sets catalogue, with mappings to standard terminologies, at this point.<span class="apple-converted-space"> </span></span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D"> </span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D">Thanks!</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D">Sina</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#1F497D"> </span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">From:</span></b></span><span style="mso-bookmark:_MailOriginalBody"><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif"> </span></span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">John
 Graybeal [</span></span><a href="mailto:jgraybeal@stanford.edu"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">mailto:jgraybeal@stanford.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Wednesday, January 31, 2018 6:50 PM<br>
<b>To:</b><span class="apple-converted-space"> </span>Michael Dorf<br>
<b>Cc:</b><span class="apple-converted-space"> </span></span></span><a href="mailto:support@bioontology.org"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">support@bioontology.org</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">;
 Madani, Sina<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Sina,<span class="apple-converted-space"> </span><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">(Changing the topic line to focus on the SPARQL question that I'm addressing here.)  <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site".<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">On BioPortal we have the 'front-end beta SPARQL query UI' set up at </span></span><a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsparql.bioontology.org&data=02%7C01%7CSina.Madani%40vumc.org%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=t2pxaHHIGDvX7Bvy7%2FCud0e0xT0h%2F7BRD6B4ctOgX%2Fs%3D&reserved=0"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:purple">http://sparql.bioontology.org</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">.
 There are a few complexities before the queries get to the backend service, which is a separate 4store service from the one used to serve BioPortal itself. (Which is why the backend data is not the same.)  We could tell you about all those details and provide
 code to make it all work, but you may not need things to be configured that way on your system.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">It is certainly possible to configure the primary backend store (4store) that your Virtual Appliance uses, so that it can accept
 queries from anywhere. If you are running a public service, you might not want to do that, because it is difficult to protect your back end from queries that can take the system down. (That's why we don't do it that way on BioPortal.)<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">I think that Clement Jonquet may have found a way to do it that doesn't have many problems, for his AgroPortal installation.
 He reads this list and will likely weigh in, but if not we can make sure he gets this question too. <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers!<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">John<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">On Jan 31, 2018, at 3:05 PM, Michael Dorf <</span></span><a href="mailto:mdorf@stanford.edu"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:purple">mdorf@stanford.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">>
 wrote:<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Hi,</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I am using a local version of Appliance 2.5 RC3 as well as UMLS2RDF script against UMLS2017AB database to generate and load SNOMED.ttl file (1.29Gb).</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">However, upon submitting a new ontology and after few seconds I get this error message in the web UI: “something went wrong”. Also,<span class="apple-converted-space"> </span></span><a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fontotoportal.admin%2F&data=02%7C01%7CSina.Madani%40vumc.org%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%3D&reserved=0"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#0B4CB4">http://ontotoportal.admin</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span class="apple-converted-space"> </span></span><span style="mso-bookmark:_MailOriginalBody">report
 under issues section shows “ontology has no submission”.  Under /srv/ncbo/repository path no directory was created for SNOMED. Seems manually creating “1” submission directory and copying SNOMED ttl into that directory doesn’t have any effect even with manual
 parsing per instruction. Is it possible to manually load large ttl files and create submissions?</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Scheduler.log or appliance.log doesn’t show any error either.</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I re-tried the submission with a compressed tar file (72 Mb) too. This time,  </span><a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fontotoportal.admin%2F&data=02%7C01%7CSina.Madani%40vumc.org%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%3D&reserved=0"><span style="mso-bookmark:_MailOriginalBody"><span style="color:#0B4CB4">http://ontotoportal.admin</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span class="apple-converted-space"> </span></span><span style="mso-bookmark:_MailOriginalBody">showed
 ERROR_RDF under Error Status field. Also, on admin page, the log link under URL field shows below messages.  It seems manually unzipping the file and/or reprocessing it doesn’t have any effect either </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Is there a workaround for loading/parsing SNOMED (or similar large ontologies) into OntoPortal? Also, is it possible to access 4store directly in our local instance from a sparql endpoint similar
 to Bioportal website?</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Thanks!</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Sina</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#262626">I, [2018-01-28T11:19:17.181176 #3910]  INFO -- : ["Starting to process<span class="apple-converted-space"> </span></span></span><a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMED%2Fsubmissions%2F1%2522&data=02%7C01%7CSina.Madani%40vumc.org%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=C7B0qSamo%2BQz%2F1zW3G41kA3FzLCGJlKPYhMdXu7G8NU%3D&reserved=0"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#0B4CB4">http://data.bioontology.org/ontologies/SNOMED/submissions/1"</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#262626">]</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#262626">I, [2018-01-28T11:19:17.219473 #3910]  INFO -- : ["Starting to process SNOMED/submissions/1"]</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#262626">I, [2018-01-28T11:19:17.338663 #3910]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"]</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#262626">E, [2018-01-28T11:19:17.338923 #3910] ERROR -- : ["ArgumentError: invalid byte sequence in UTF-8\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:398:in
 `block in generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `foreach'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in
 `generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:414:in `generate_rdf'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:903:in
 `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in
 `each'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/bin/ncbo_cron:228:in `block (3 levels) in <main>'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in
 scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in
 `lock'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:230:in
 `trigger_block'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:204:in `block in trigger'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/scheduler.rb:430:in `block in
 trigger_job'"]</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> </span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">_______________________________________________<br>
bioontology-support mailing list<br>
</span></span><a href="mailto:bioontology-support@lists.stanford.edu"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:purple">bioontology-support@lists.stanford.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><br>
</span></span><a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7CSina.Madani%40vumc.org%7Cff6db93c5608494ba5e908d56a0e8238%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636531532933146046&sdata=JFjyDOXVhifeBqHTHXeb0UdQLlcFXmPU9It5aHW%2B%2BNU%3D&reserved=0"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:purple">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">========================<span class="apple-converted-space"> </span><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">John Graybeal<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Technical Program Manager<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal<o:p></o:p></span></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Stanford Center for Biomedical Informatics Research<br>
650-736-1632<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:black">========================
<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:black">John Graybeal<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:black">Technical Program Manager<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="color:black">Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal<o:p></o:p></span></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="mso-bookmark:_MailOriginalBody"><span style="color:black">Stanford Center for Biomedical Informatics Research<br>
650-736-1632<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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