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<p class="MsoNormal">Hi, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have another question while support is working on my previous one
<span style="font-family:"Apple Color Emoji"">☺</span> <o:p></o:p></p>
<p class="MsoNormal">If I provide a linkage between two classes from two ontologies through skos:exactMatch (or other mapping types) in my TTL file, does such linkage appear (under mapping) in Ontoportal when I load the ttl as an ontology submission in our
 local appliance instance ? is it possible to map two classes within the same ontology?
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks!<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">Michael Dorf <mdorf@stanford.edu><br>
<b>Date: </b>Wednesday, January 31, 2018 at 6:05 PM<br>
<b>To: </b>"support@bioontology.org" <support@bioontology.org><br>
<b>Cc: </b>"Madani, Sina" <Sina.Madani@vumc.org><br>
<b>Subject: </b>Fwd: [bioontology-support] search by id in a subtree<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,</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><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%7C554ad71a7e0a46378dd108d568ff2dba%7Cfaf5c158acd1455587833814469e1079%7C0%7C1%7C636530367560770166&sdata=lpdE66Y3XQeJp2WNmjiADZMPndyQHkIVJkLobpX8dMs%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%7C554ad71a7e0a46378dd108d568ff2dba%7Cfaf5c158acd1455587833814469e1079%7C0%7C1%7C636530367560770166&sdata=lpdE66Y3XQeJp2WNmjiADZMPndyQHkIVJkLobpX8dMs%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"> </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:Menlo-Regular;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%7C554ad71a7e0a46378dd108d568ff2dba%7Cfaf5c158acd1455587833814469e1079%7C0%7C1%7C636530367560770166&sdata=yJHa7HWVveLBiZSZPGFjFwBzBOrvErAiU%2Fk6aCHmMBo%3D&reserved=0"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Menlo-Regular;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:Menlo-Regular;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:Menlo-Regular;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:Menlo-Regular;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:Menlo-Regular;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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