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[bioontology-support] Question about processing UMLS ontologies

Koo, Jahoon JAHOON.KOO at UCDENVER.EDU
Fri Mar 27 14:08:29 PDT 2020


John,

I was able to migrate some UMLS and non-UMLS ontologies through the UI without any problems and I can see everything normally in my virtual appliance.
I really appreciate the troubleshooting guide you provided.

Currently, I am trying to upload SNOMEDCT_US.ttl file through the UI. However, when I upload the ttl file to my instance, I get “We're sorry but something has gone wrong. We have been notified of this error” on the UI, and there is no log in the admin page. Also, I don’t see a SNOMEDCT directory in the /srv/ncbo/repository directory. I have attached a screenshot of the ontologies api log file to this email.
I tried to open the ttl file in Protégé to check if it was parsed properly, but it took too long to load and just froze.

Can you please help me migrating SNOMEDCT?

Thank you.
Jahoon

From: John Graybeal <jgraybeal at stanford.edu>
Sent: Tuesday, March 10, 2020 9:28 PM
To: Koo, Jahoon <JAHOON.KOO at UCDENVER.EDU>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Question about processing UMLS ontologies

Jahoon,

Michael did a good job summarizing the challenges for us. As manager I have a bit of discretion, so I'll jump in where I can, but right now we can't provide direct support of your work. My apologies for that, but part of the reason for the list is that other people who have had similar issues may be able to help as well.

I appreciate the screen shot and additional details you have offered they are very important. It is very difficult to solve these problems remotely, and it is impossible if you only provide an error message without screenshots (of both the submission process you performed, and of the displays that result) and log data. The log data and screenshot you've offered have been a good start; more precise requests are in the steps below.

Congratulations on parsing the UMLS data into TTL files, I'm sure it took a while! I can confirm that uploading the TTL should work on these ontologies, it is compatible with the OWLAPI library we use and we have successfully loaded other TTL files.

These are the things I would do if I were in your situation. If you do these things, it will help you at least narrow down the nature of the problem.  (Ideally this will become part of our on-line documentation soon!)

1) Take a simple non-UMLS ontology (can use one from BioPortal) and load it. Confirm that you can see everything normally in the UI (look at the classes list in particular), and that you can see appropriate entries in the /srv/ncbo/ontologies_api/shared/log directory (mainly the 404 'not found' errors at the end of some lines should be replaced by 200 'status OK' values), and in the /srv/ncbo/repository directory.

2) Take the smallest TTL file that you want to upload. Examine the text file, confirm that lines look reasonable and that the last line is not incomplete. Open this TTL file in Protege to confirm it will parse correctly. Verify that the expected classes (as seen in BioPortal) can be seen in Protege. If the TTL file can not be fully opened in Protege, then something in the UMLS translation did not work. We have no experience here, but someone else may.

3) Assuming Protege opens the TTL file without issue, submit the TTL file manually to your system. This process should work the same as step 1 and you can verify it the same way. If the first file fails, go to step 4.  If the first file succeeds, proceed one file at a time to see which files succeed and which files fail. This will give you a clue where any problem lies (big files, many or few files, etc.—if it's just one file try submitting it to BioPortal to see if that passes). Try step 2 with any files that fail—if they can not be opened with Protege, BioPortal can not open them either. If their last line is abruptly terminated, that would get us closer. Detailed information about that failure on the Bioportal list might elicit a clue from someone else who has gone through this process.

4) Examine the logs of the submission process by using the Admin page of your BioPortal instance (be sure you are logged in as an administrator), the Ontology Administration page (see image; note the Filter field helps you see specific rows). The "Log" hyperlink shows logs of the submission processes that happens; below I've copied our log of this from BioPortal. See what looks the same and what looks different; the pattern is largely the same for all ontologies, and you can view the logs of your successful submissions for comparison. (Note the 'diff' command failed, and some indexing commands had issues, in our log; I'm not sure why but these will not be relevant to your problem.)  You can probably guess where the issue first occurred from close examination of that log, but if you send that log to us we can guess what might be happening, especially if you send us screen shots of the submission screen (before you click Submit), the directory listing of the submissions directory where the submission should appear (or the parent directory if the submission hasn't appeared) and the error log.

5) Once you have isolated the problem to the exact thing that isn't working, and created an appropriate report with pictures and logs, we or others may be able to help relatively quickly with that problem. We appreciate your patience if we can not respond quickly, and in that case we encourage you to continue diving into the system from your side to understand what is going on.

These are sophisticated and challenging systems that have shared community ownership, so I trust your persistence will be rewarded in due course. You may find revisiting all the Virtual Appliance help pages<https://www.bioontology.org/wiki/Category:NCBO_Virtual_Appliance> (see list at the end of that link) helps you put everything in context as you are continuing your troubleshooting.

John





[cid:image001.png at 01D60449.A66244B0]

Parse Log for ICD9CM


Log file: ICD9CM/17/parsing.log

# Logfile created on 2019-11-18 20:02:07 -0800 by logger.rb/v1.4.1

I, [2019-11-18T20:02:07.512450 #5869]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-18T20:02:07.535157 #5869]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-18T20:02:07.730390 #5869]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"]

I, [2019-11-18T20:02:13.484800 #5869]  INFO -- : ["Triples /srv/ncbo/repository/ICD9CM/17/ICD9CM.ttl appended in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:14.320945 #5869]  INFO -- : ["17: page 1 of 10 - 2500 ontology terms retrieved in 0.69387213 sec."]

I, [2019-11-18T20:02:15.824989 #5869]  INFO -- : ["No labels generated in page 1."]

I, [2019-11-18T20:02:15.825102 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:16.038064 #5869]  INFO -- : ["Mapping labels asserted in 0.210233705 sec."]

I, [2019-11-18T20:02:16.587712 #5869]  INFO -- : ["17: page 2 of 10 - 2500 ontology terms retrieved in 0.549526678 sec."]

I, [2019-11-18T20:02:18.134307 #5869]  INFO -- : ["No labels generated in page 2."]

I, [2019-11-18T20:02:18.134387 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:18.352864 #5869]  INFO -- : ["Mapping labels asserted in 0.215125578 sec."]

I, [2019-11-18T20:02:18.855389 #5869]  INFO -- : ["17: page 3 of 10 - 2500 ontology terms retrieved in 0.502395089 sec."]

I, [2019-11-18T20:02:20.464175 #5869]  INFO -- : ["No labels generated in page 3."]

I, [2019-11-18T20:02:20.464284 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:20.678632 #5869]  INFO -- : ["Mapping labels asserted in 0.211600159 sec."]

I, [2019-11-18T20:02:21.177049 #5869]  INFO -- : ["17: page 4 of 10 - 2500 ontology terms retrieved in 0.498294527 sec."]

I, [2019-11-18T20:02:22.747688 #5869]  INFO -- : ["No labels generated in page 4."]

I, [2019-11-18T20:02:22.747787 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:22.965751 #5869]  INFO -- : ["Mapping labels asserted in 0.214613798 sec."]

I, [2019-11-18T20:02:23.549835 #5869]  INFO -- : ["17: page 5 of 10 - 2500 ontology terms retrieved in 0.583966778 sec."]

I, [2019-11-18T20:02:25.106772 #5869]  INFO -- : ["No labels generated in page 5."]

I, [2019-11-18T20:02:25.106862 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:25.417500 #5869]  INFO -- : ["Mapping labels asserted in 0.306262085 sec."]

I, [2019-11-18T20:02:25.955334 #5869]  INFO -- : ["17: page 6 of 10 - 2500 ontology terms retrieved in 0.537712308 sec."]

I, [2019-11-18T20:02:27.567768 #5869]  INFO -- : ["No labels generated in page 6."]

I, [2019-11-18T20:02:27.567847 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:27.799703 #5869]  INFO -- : ["Mapping labels asserted in 0.22695519 sec."]

I, [2019-11-18T20:02:28.326090 #5869]  INFO -- : ["17: page 7 of 10 - 2500 ontology terms retrieved in 0.526264929 sec."]

I, [2019-11-18T20:02:29.982127 #5869]  INFO -- : ["No labels generated in page 7."]

I, [2019-11-18T20:02:29.982235 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:30.221938 #5869]  INFO -- : ["Mapping labels asserted in 0.234746836 sec."]

I, [2019-11-18T20:02:30.750091 #5869]  INFO -- : ["17: page 8 of 10 - 2500 ontology terms retrieved in 0.528025614 sec."]

I, [2019-11-18T20:02:32.406697 #5869]  INFO -- : ["No labels generated in page 8."]

I, [2019-11-18T20:02:32.406797 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:32.635639 #5869]  INFO -- : ["Mapping labels asserted in 0.224060082 sec."]

I, [2019-11-18T20:02:33.165793 #5869]  INFO -- : ["17: page 9 of 10 - 2500 ontology terms retrieved in 0.530015955 sec."]

I, [2019-11-18T20:02:34.824474 #5869]  INFO -- : ["No labels generated in page 9."]

I, [2019-11-18T20:02:34.824567 #5869]  INFO -- : ["Asserting 5002 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:35.056265 #5869]  INFO -- : ["Mapping labels asserted in 0.226847435 sec."]

I, [2019-11-18T20:02:35.096220 #5869]  INFO -- : ["17: page 10 of 10 - 33 ontology terms retrieved in 0.039867943 sec."]

I, [2019-11-18T20:02:36.350747 #5869]  INFO -- : ["No labels generated in page 10."]

I, [2019-11-18T20:02:36.350851 #5869]  INFO -- : ["Asserting 68 mappings in <http://data.bioontology.org/ontologies/ICD9CM/submissions/17>"]

I, [2019-11-18T20:02:36.411246 #5869]  INFO -- : ["Mapping labels asserted in 0.057513075 sec."]

I, [2019-11-18T20:02:36.411306 #5869]  INFO -- : ["end generate_missing_labels traversed 22533 classes"]

I, [2019-11-18T20:02:36.411340 #5869]  INFO -- : ["Saved generated labels in /srv/ncbo/repository/ICD9CM/17/labels.ttl"]

I, [2019-11-18T20:02:36.411803 #5869]  INFO -- : ["Completed Missing Labels Generation: 17 in 22.83837378300086 sec. 22533 classes."]

I, [2019-11-18T20:02:36.585559 #5869]  INFO -- : ["metrics_for_submission start"]

I, [2019-11-18T20:02:36.919292 #5869]  INFO -- : ["Metrics groupby_children retrieved 4003 in 0.205420133 sec."]

I, [2019-11-18T20:02:36.921578 #5869]  INFO -- : ["Metrics count_classes retrieved 22533 in 0.000689756 sec."]

I, [2019-11-18T20:02:36.945947 #5869]  INFO -- : ["Metrics count cls with def 0 in 0.024288923 sec."]

I, [2019-11-18T20:02:36.946235 #5869]  INFO -- : ["Class metrics finished in 0.360602243 sec."]

I, [2019-11-18T20:02:36.946275 #5869]  INFO -- : ["class_metrics finished"]

I, [2019-11-18T20:02:36.946772 #5869]  INFO -- : ["individuals finished"]

I, [2019-11-18T20:02:36.947167 #5869]  INFO -- : ["properties finished"]

I, [2019-11-18T20:02:36.948358 #5869]  INFO -- : ["generation of metrics file finished"]

I, [2019-11-18T20:02:37.191197 #5869]  INFO -- : ["Java call [java -DentityExpansionLimit=1500000 -Xmx5120M -jar /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/bin/bubastis.jar -ontology1 /srv/ncbo/repository/ICD9CM/16/ICD9CM.ttl -ontology2 /srv/ncbo/repository/ICD9CM/17/ICD9CM.ttl -output /srv/ncbo/repository/ICD9CM/17/bubastis_diff.xml -format xml]"]

I, [2019-11-18T20:02:38.744496 #5869]  INFO -- : ["Bubastis diff finished OK."]

I, [2019-11-18T20:02:38.744557 #5869]  INFO -- : ["Performing diff failed.  Reason: null\n"]

I, [2019-11-18T20:02:38.744625 #5869]  INFO -- : ["ontology 1 is a file /srv/ncbo/repository/ICD9CM/16/ICD9CM.ttl\nontology 2 is a file /srv/ncbo/repository/ICD9CM/17/ICD9CM.ttl\ntrying load now\n"]

E, [2019-11-18T20:02:38.745114 #5869] ERROR -- : ["Bubastis diff for http://data.bioontology.org/ontologies/ICD9CM/submissions/17 failed - LinkedData::Diff::BubastisDiffException: Bubastis diff command exited with status=0. Output file /srv/ncbo/repository/ICD9CM/17/bubastis_diff.xml cannot be found."]

E, [2019-11-18T20:02:38.745269 #5869] ERROR -- : ["LinkedData::Diff::BubastisDiffException: Bubastis diff command exited with status=0. Output file /srv/ncbo/repository/ICD9CM/17/bubastis_diff.xml cannot be found.\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/diff/bubastis_diff.rb:100:in `call_bubastis_java_cmd'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/diff/bubastis_diff.rb:114:in `diff'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:340:in `diff'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1090:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t./bin/ncbo_ontology_process:98:in `block in <main>'\n\t./bin/ncbo_ontology_process:81:in `each'\n\t./bin/ncbo_ontology_process:81:in `<main>'"]

I, [2019-11-18T20:02:38.835827 #5869]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-18T20:02:38.849751 #5869] DEBUG -- : ["Archiving submissions previous to http://data.bioontology.org/ontologies/ICD9CM/submissions/17..."]

I, [2019-11-18T20:02:38.945586 #5869]  INFO -- : ["Starting to process ICD9CM/submissions/16"]

I, [2019-11-18T20:02:39.073811 #5869]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/16 completed successfully"]

D, [2019-11-18T20:02:39.078274 #5869] DEBUG -- : ["Completed archiving submissions previous to http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

D, [2019-11-18T20:02:39.078335 #5869] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 31.64s"]

I, [2019-11-18T20:02:39.098572 #5869]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-18T20:02:39.098620 #5869]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-18T20:02:39.552309 #5869]  INFO -- : ["Finished report for ICD9CM in 0.45357125499867834 sec."]

I, [2019-11-18T20:02:39.579672 #5869]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-19T13:13:49.414900 #1305]  INFO -- : ["Caching classes of ICD9CM"]

I, [2019-11-19T13:13:50.346732 #1305]  INFO -- : ["Page 1 of 10 - 2500 classes retrieved in 0.926725123 sec."]

I, [2019-11-19T13:13:52.107605 #1305]  INFO -- : ["Page 1 of 10 cached in Annotator in 1.760705514 sec."]

I, [2019-11-19T13:13:52.851484 #1305]  INFO -- : ["Page 2 of 10 - 2500 classes retrieved in 0.743708626 sec."]

I, [2019-11-19T13:13:54.531517 #1305]  INFO -- : ["Page 2 of 10 cached in Annotator in 1.679857612 sec."]

I, [2019-11-19T13:13:55.985973 #1305]  INFO -- : ["Page 3 of 10 - 2500 classes retrieved in 1.454251696 sec."]

I, [2019-11-19T13:13:59.021801 #1305]  INFO -- : ["Page 3 of 10 cached in Annotator in 3.035339432 sec."]

I, [2019-11-19T13:13:59.762575 #1305]  INFO -- : ["Page 4 of 10 - 2500 classes retrieved in 0.740614706 sec."]

I, [2019-11-19T13:14:02.391035 #1305]  INFO -- : ["Page 4 of 10 cached in Annotator in 2.628320488 sec."]

I, [2019-11-19T13:14:03.151625 #1305]  INFO -- : ["Page 5 of 10 - 2500 classes retrieved in 0.760251509 sec."]

I, [2019-11-19T13:14:06.395942 #1305]  INFO -- : ["Page 5 of 10 cached in Annotator in 3.244110993 sec."]

I, [2019-11-19T13:14:07.281154 #1305]  INFO -- : ["Page 6 of 10 - 2500 classes retrieved in 0.88502673 sec."]

I, [2019-11-19T13:14:10.556262 #1305]  INFO -- : ["Page 6 of 10 cached in Annotator in 3.27473589 sec."]

I, [2019-11-19T13:14:11.405121 #1305]  INFO -- : ["Page 7 of 10 - 2500 classes retrieved in 0.848712592 sec."]

I, [2019-11-19T13:14:14.464392 #1305]  INFO -- : ["Page 7 of 10 cached in Annotator in 3.059119161 sec."]

I, [2019-11-19T13:14:15.355936 #1305]  INFO -- : ["Page 8 of 10 - 2500 classes retrieved in 0.891182191 sec."]

I, [2019-11-19T13:14:18.269290 #1305]  INFO -- : ["Page 8 of 10 cached in Annotator in 2.913212045 sec."]

I, [2019-11-19T13:14:19.054914 #1305]  INFO -- : ["Page 9 of 10 - 2500 classes retrieved in 0.785449949 sec."]

I, [2019-11-19T13:14:22.807811 #1305]  INFO -- : ["Page 9 of 10 cached in Annotator in 3.752741496 sec."]

I, [2019-11-19T13:14:22.888491 #1305]  INFO -- : ["Page 10 of 10 - 33 classes retrieved in 0.08012711 sec."]

I, [2019-11-19T13:14:22.917793 #1305]  INFO -- : ["Page 10 of 10 cached in Annotator in 0.029105371 sec."]

I, [2019-11-19T13:14:23.070232 #1305]  INFO -- : ["Completed caching ontology: ICD9CM (http://data.bioontology.org/ontologies/ICD9CM/submissions/17) in 33.50305255400599 sec. 22533 classes."]

I, [2019-11-20T08:39:43.612549 #7883]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-20T08:39:43.639090 #7883]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-20T08:39:43.645578 #7883]  INFO -- : ["Indexing ontology terms: ICD9CM..."]

E, [2019-11-20T08:39:43.647805 #7883] ERROR -- : ["RSolr::Error::Http: RSolr::Error::Http - 400 Bad Request\nError: {\n  \"responseHeader\":{\n    \"status\":400,\n    \"QTime\":0},\n  \"error\":{\n    \"metadata\":[\n      \"error-class\",\"org.apache.solr.common.SolrException\",\n      \"root-error-class\",\"org.apache.solr.common.SolrException\"],\n    \"msg\":\"undefined field submissionAcronym\",\n    \"code\":400}}\n\nURI: http://ncbo-prd-sol-01.stanford.edu:8983/solr/term_search_core2/update?wt=json\nRequest Headers: {\"Content-Type\"=>\"application/json\"}\nRequest Data: \"{\\\"delete\\\":{\\\"query\\\":\\\"submissionAcronym:ICD9CM\\\"}}\"\n\nBacktrace: /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:206:in `rescue in execute'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:196:in `execute'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:191:in `send_and_receive'\n(eval):2:in `post'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:94:in `update'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:157:in `delete_by_query'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/goo-813f5c5c4e47/lib/goo/search/search.rb:82:in `unindexByQuery'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:425:in `unindex_by_acronym'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:415:in `unindex'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1145:in `block in index'\n/usr/local/rbenv/versions/2.5.6/lib/ruby/2.5.0/benchmark.rb:308:in `realtime'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:206:in `rescue in execute'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:196:in `execute'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:191:in `send_and_receive'\n\t(eval):2:in `post'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:94:in `update'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:157:in `delete_by_query'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/goo-813f5c5c4e47/lib/goo/search/search.rb:82:in `unindexByQuery'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:425:in `unindex_by_acronym'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:415:in `unindex'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1145:in `block in index'\n\t/usr/local/rbenv/versions/2.5.6/lib/ruby/2.5.0/benchmark.rb:308:in `realtime'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1139:in `index'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1025:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\tbin/ncbo_ontology_index:105:in `index_ontology'\n\tbin/ncbo_ontology_index:164:in `block (2 levels) in <main>'\n\tbin/ncbo_ontology_index:163:in `each'\n\tbin/ncbo_ontology_index:163:in `block in <main>'\n\t/usr/local/rbenv/versions/2.5.6/lib/ruby/2.5.0/benchmark.rb:308:in `realtime'\n\tbin/ncbo_ontology_index:154:in `<main>'"]

I, [2019-11-20T08:39:43.758958 #7883]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-20T08:39:43.778775 #7883] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 0.24s"]

I, [2019-11-20T08:39:43.810378 #7883]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-20T08:39:43.810432 #7883]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-20T11:45:20.255070 #19191]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-20T11:45:20.257288 #19191]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-20T11:45:20.259071 #19191]  INFO -- : ["Indexing ontology terms: ICD9CM..."]

E, [2019-11-20T11:45:20.261311 #19191] ERROR -- : ["RSolr::Error::Http: RSolr::Error::Http - 400 Bad Request\nError: {\n  \"responseHeader\":{\n    \"status\":400,\n    \"QTime\":0},\n  \"error\":{\n    \"metadata\":[\n      \"error-class\",\"org.apache.solr.common.SolrException\",\n      \"root-error-class\",\"org.apache.solr.common.SolrException\"],\n    \"msg\":\"undefined field submissionAcronym\",\n    \"code\":400}}\n\nURI: http://ncbo-prd-sol-01.stanford.edu:8983/solr/term_search_core2/update?wt=json\nRequest Headers: {\"Content-Type\"=>\"application/json\"}\nRequest Data: \"{\\\"delete\\\":{\\\"query\\\":\\\"submissionAcronym:ICD9CM\\\"}}\"\n\nBacktrace: /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:206:in `rescue in execute'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:196:in `execute'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:191:in `send_and_receive'\n(eval):2:in `post'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:94:in `update'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:157:in `delete_by_query'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/goo-813f5c5c4e47/lib/goo/search/search.rb:82:in `unindexByQuery'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:425:in `unindex_by_acronym'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:415:in `unindex'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1145:in `block in index'\n/usr/local/rbenv/versions/2.5.6/lib/ruby/2.5.0/benchmark.rb:308:in `realtime'\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:206:in `rescue in execute'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:196:in `execute'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:191:in `send_and_receive'\n\t(eval):2:in `post'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:94:in `update'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/gems/rsolr-2.2.1/lib/rsolr/client.rb:157:in `delete_by_query'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/goo-813f5c5c4e47/lib/goo/search/search.rb:82:in `unindexByQuery'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:425:in `unindex_by_acronym'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology.rb:415:in `unindex'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1145:in `block in index'\n\t/usr/local/rbenv/versions/2.5.6/lib/ruby/2.5.0/benchmark.rb:308:in `realtime'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1139:in `index'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.5.0/bundler/gems/ontologies_linked_data-57e648194224/lib/ontologies_linked_data/models/ontology_submission.rb:1025:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\tbin/ncbo_ontology_index:105:in `index_ontology'\n\tbin/ncbo_ontology_index:164:in `block (2 levels) in <main>'\n\tbin/ncbo_ontology_index:163:in `each'\n\tbin/ncbo_ontology_index:163:in `block in <main>'\n\t/usr/local/rbenv/versions/2.5.6/lib/ruby/2.5.0/benchmark.rb:308:in `realtime'\n\tbin/ncbo_ontology_index:154:in `<main>'"]

I, [2019-11-20T11:45:20.465715 #19191]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-20T11:45:20.474991 #19191] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 0.33s"]

I, [2019-11-20T11:45:20.498082 #19191]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-20T11:45:20.498131 #19191]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-20T16:10:00.540334 #31955]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-20T16:10:00.574226 #31955]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-20T16:10:00.580196 #31955]  INFO -- : ["Indexing ontology terms: ICD9CM..."]

I, [2019-11-20T16:10:00.592327 #31955]  INFO -- : ["Removed ontology terms index (0.01201467s)"]

I, [2019-11-20T16:10:02.353084 #31955]  INFO -- : ["Thread 1: Page 1 of 23 - 1000 ontology terms retrieved in 8.701e-06 sec."]

I, [2019-11-20T16:10:02.778423 #31955]  INFO -- : ["Thread 1: Page 1 of 23 attributes mapped in 0.425212379 sec."]

I, [2019-11-20T16:10:11.828062 #31955]  INFO -- : ["Thread 1: Page 1 of 23 - 1000 ontology terms indexed in 9.049491852 sec."]

I, [2019-11-20T16:10:12.950236 #31955]  INFO -- : ["Thread 1: Page 2 of 23 - 1000 ontology terms retrieved in 8.735e-06 sec."]

I, [2019-11-20T16:10:13.364981 #31955]  INFO -- : ["Thread 1: Page 2 of 23 attributes mapped in 0.414563531 sec."]

I, [2019-11-20T16:10:20.681383 #31955]  INFO -- : ["Thread 1: Page 2 of 23 - 1000 ontology terms indexed in 7.316251346 sec."]

I, [2019-11-20T16:10:22.052976 #31955]  INFO -- : ["Thread 1: Page 3 of 23 - 1000 ontology terms retrieved in 7.498e-06 sec."]

I, [2019-11-20T16:10:22.546871 #31955]  INFO -- : ["Thread 1: Page 3 of 23 attributes mapped in 0.4937684 sec."]

I, [2019-11-20T16:10:29.545338 #31955]  INFO -- : ["Thread 1: Page 3 of 23 - 1000 ontology terms indexed in 6.998329012 sec."]

I, [2019-11-20T16:10:30.684326 #31955]  INFO -- : ["Thread 1: Page 4 of 23 - 1000 ontology terms retrieved in 7.089e-06 sec."]

I, [2019-11-20T16:10:31.087242 #31955]  INFO -- : ["Thread 1: Page 4 of 23 attributes mapped in 0.402795127 sec."]

I, [2019-11-20T16:10:37.913014 #31955]  INFO -- : ["Thread 1: Page 4 of 23 - 1000 ontology terms indexed in 6.825633879 sec."]

I, [2019-11-20T16:10:39.470693 #31955]  INFO -- : ["Thread 1: Page 5 of 23 - 1000 ontology terms retrieved in 7.658e-06 sec."]

I, [2019-11-20T16:10:39.925554 #31955]  INFO -- : ["Thread 1: Page 5 of 23 attributes mapped in 0.45470115 sec."]

I, [2019-11-20T16:10:45.881535 #31955]  INFO -- : ["Thread 1: Page 5 of 23 - 1000 ontology terms indexed in 5.95583884 sec."]

I, [2019-11-20T16:10:46.952455 #31955]  INFO -- : ["Thread 1: Page 6 of 23 - 1000 ontology terms retrieved in 7.296e-06 sec."]

I, [2019-11-20T16:10:47.362203 #31955]  INFO -- : ["Thread 1: Page 6 of 23 attributes mapped in 0.409378311 sec."]

I, [2019-11-20T16:10:53.784437 #31955]  INFO -- : ["Thread 1: Page 6 of 23 - 1000 ontology terms indexed in 6.422088928 sec."]

I, [2019-11-20T16:10:54.930537 #31955]  INFO -- : ["Thread 1: Page 7 of 23 - 1000 ontology terms retrieved in 8.153e-06 sec."]

I, [2019-11-20T16:10:55.425453 #31955]  INFO -- : ["Thread 1: Page 7 of 23 attributes mapped in 0.494520025 sec."]

I, [2019-11-20T16:11:01.605643 #31955]  INFO -- : ["Thread 1: Page 7 of 23 - 1000 ontology terms indexed in 6.180050321 sec."]

I, [2019-11-20T16:11:03.019251 #31955]  INFO -- : ["Thread 1: Page 8 of 23 - 1000 ontology terms retrieved in 8.607e-06 sec."]

I, [2019-11-20T16:11:03.419231 #31955]  INFO -- : ["Thread 1: Page 8 of 23 attributes mapped in 0.399574646 sec."]

I, [2019-11-20T16:11:09.073943 #31955]  INFO -- : ["Thread 1: Page 8 of 23 - 1000 ontology terms indexed in 5.654564128 sec."]

I, [2019-11-20T16:11:11.470516 #31955]  INFO -- : ["Thread 1: Page 9 of 23 - 1000 ontology terms retrieved in 7.681e-06 sec."]

I, [2019-11-20T16:11:11.972205 #31955]  INFO -- : ["Thread 1: Page 9 of 23 attributes mapped in 0.501262563 sec."]

I, [2019-11-20T16:11:19.871747 #31955]  INFO -- : ["Thread 1: Page 9 of 23 - 1000 ontology terms indexed in 7.899397483 sec."]

I, [2019-11-20T16:11:20.992328 #31955]  INFO -- : ["Thread 1: Page 10 of 23 - 1000 ontology terms retrieved in 8.061e-06 sec."]

I, [2019-11-20T16:11:21.395213 #31955]  INFO -- : ["Thread 1: Page 10 of 23 attributes mapped in 0.402746955 sec."]

I, [2019-11-20T16:11:27.697053 #31955]  INFO -- : ["Thread 1: Page 10 of 23 - 1000 ontology terms indexed in 6.301697787 sec."]

I, [2019-11-20T16:11:28.866376 #31955]  INFO -- : ["Thread 1: Page 11 of 23 - 1000 ontology terms retrieved in 8.812e-06 sec."]

I, [2019-11-20T16:11:29.356955 #31955]  INFO -- : ["Thread 1: Page 11 of 23 attributes mapped in 0.490177393 sec."]

I, [2019-11-20T16:11:35.221824 #31955]  INFO -- : ["Thread 1: Page 11 of 23 - 1000 ontology terms indexed in 5.864728349 sec."]

I, [2019-11-20T16:11:36.356943 #31955]  INFO -- : ["Thread 1: Page 12 of 23 - 1000 ontology terms retrieved in 8.023e-06 sec."]

I, [2019-11-20T16:11:36.761940 #31955]  INFO -- : ["Thread 1: Page 12 of 23 attributes mapped in 0.404646063 sec."]

I, [2019-11-20T16:11:42.310600 #31955]  INFO -- : ["Thread 1: Page 12 of 23 - 1000 ontology terms indexed in 5.548524638 sec."]

I, [2019-11-20T16:11:43.514308 #31955]  INFO -- : ["Thread 1: Page 13 of 23 - 1000 ontology terms retrieved in 7.857e-06 sec."]

I, [2019-11-20T16:11:44.002224 #31955]  INFO -- : ["Thread 1: Page 13 of 23 attributes mapped in 0.487459615 sec."]

I, [2019-11-20T16:11:50.589594 #31955]  INFO -- : ["Thread 1: Page 13 of 23 - 1000 ontology terms indexed in 6.587225467 sec."]

I, [2019-11-20T16:11:51.701078 #31955]  INFO -- : ["Thread 1: Page 14 of 23 - 1000 ontology terms retrieved in 7.584e-06 sec."]

I, [2019-11-20T16:11:52.107673 #31955]  INFO -- : ["Thread 1: Page 14 of 23 attributes mapped in 0.406461343 sec."]

I, [2019-11-20T16:11:57.959994 #31955]  INFO -- : ["Thread 1: Page 14 of 23 - 1000 ontology terms indexed in 5.852167832 sec."]

I, [2019-11-20T16:11:59.215228 #31955]  INFO -- : ["Thread 1: Page 15 of 23 - 1000 ontology terms retrieved in 7.685e-06 sec."]

I, [2019-11-20T16:11:59.635655 #31955]  INFO -- : ["Thread 1: Page 15 of 23 attributes mapped in 0.420024 sec."]

I, [2019-11-20T16:12:05.339223 #31955]  INFO -- : ["Thread 1: Page 15 of 23 - 1000 ontology terms indexed in 5.703394833 sec."]

I, [2019-11-20T16:12:06.480823 #31955]  INFO -- : ["Thread 1: Page 16 of 23 - 1000 ontology terms retrieved in 7.881e-06 sec."]

I, [2019-11-20T16:12:06.885257 #31955]  INFO -- : ["Thread 1: Page 16 of 23 attributes mapped in 0.404082261 sec."]

I, [2019-11-20T16:12:12.638932 #31955]  INFO -- : ["Thread 1: Page 16 of 23 - 1000 ontology terms indexed in 5.753531322 sec."]

I, [2019-11-20T16:12:13.926947 #31955]  INFO -- : ["Thread 1: Page 17 of 23 - 1000 ontology terms retrieved in 7.648e-06 sec."]

I, [2019-11-20T16:12:14.325747 #31955]  INFO -- : ["Thread 1: Page 17 of 23 attributes mapped in 0.398438095 sec."]

I, [2019-11-20T16:12:20.056132 #31955]  INFO -- : ["Thread 1: Page 17 of 23 - 1000 ontology terms indexed in 5.730239902 sec."]

I, [2019-11-20T16:12:21.282556 #31955]  INFO -- : ["Thread 1: Page 18 of 23 - 1000 ontology terms retrieved in 7.797e-06 sec."]

I, [2019-11-20T16:12:21.686154 #31955]  INFO -- : ["Thread 1: Page 18 of 23 attributes mapped in 0.403440579 sec."]

I, [2019-11-20T16:12:27.520090 #31955]  INFO -- : ["Thread 1: Page 18 of 23 - 1000 ontology terms indexed in 5.833789128 sec."]

I, [2019-11-20T16:12:28.795681 #31955]  INFO -- : ["Thread 1: Page 19 of 23 - 1000 ontology terms retrieved in 7.557e-06 sec."]

I, [2019-11-20T16:12:29.195848 #31955]  INFO -- : ["Thread 1: Page 19 of 23 attributes mapped in 0.400042368 sec."]

I, [2019-11-20T16:12:35.316932 #31955]  INFO -- : ["Thread 1: Page 19 of 23 - 1000 ontology terms indexed in 6.120938664 sec."]

I, [2019-11-20T16:12:36.458359 #31955]  INFO -- : ["Thread 1: Page 20 of 23 - 1000 ontology terms retrieved in 7.337e-06 sec."]

I, [2019-11-20T16:12:36.950214 #31955]  INFO -- : ["Thread 1: Page 20 of 23 attributes mapped in 0.491720148 sec."]

I, [2019-11-20T16:12:42.400377 #31955]  INFO -- : ["Thread 1: Page 20 of 23 - 1000 ontology terms indexed in 5.450031066 sec."]

I, [2019-11-20T16:12:43.483033 #31955]  INFO -- : ["Thread 1: Page 21 of 23 - 1000 ontology terms retrieved in 7.552e-06 sec."]

I, [2019-11-20T16:12:43.881860 #31955]  INFO -- : ["Thread 1: Page 21 of 23 attributes mapped in 0.398704173 sec."]

I, [2019-11-20T16:12:50.475098 #31955]  INFO -- : ["Thread 1: Page 21 of 23 - 1000 ontology terms indexed in 6.593073418 sec."]

I, [2019-11-20T16:12:51.713574 #31955]  INFO -- : ["Thread 1: Page 22 of 23 - 1000 ontology terms retrieved in 8.22e-06 sec."]

I, [2019-11-20T16:12:52.178317 #31955]  INFO -- : ["Thread 1: Page 22 of 23 attributes mapped in 0.464622502 sec."]

I, [2019-11-20T16:12:58.460298 #31955]  INFO -- : ["Thread 1: Page 22 of 23 - 1000 ontology terms indexed in 6.28182809 sec."]

I, [2019-11-20T16:12:59.102649 #31955]  INFO -- : ["Thread 1: Page 23 of 23 - 533 ontology terms retrieved in 7.752e-06 sec."]

I, [2019-11-20T16:12:59.308354 #31955]  INFO -- : ["Thread 1: Page 23 of 23 attributes mapped in 0.205559449 sec."]

I, [2019-11-20T16:13:02.029284 #31955]  INFO -- : ["Thread 1: Page 23 of 23 - 533 ontology terms indexed in 2.720782777 sec."]

I, [2019-11-20T16:13:02.403657 #31955]  INFO -- : ["Ontology terms index commit in 0.370600725 sec."]

I, [2019-11-20T16:13:02.403826 #31955]  INFO -- : ["Completed indexing ontology terms: ICD9CM in 181.82873972100788 sec. 22533 classes."]

I, [2019-11-20T16:13:02.518306 #31955]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-20T16:13:02.533670 #31955] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 182.09s"]

I, [2019-11-20T16:13:02.558112 #31955]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-20T16:13:02.558209 #31955]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-20T16:13:03.095281 #31955]  INFO -- : ["Finished report for ICD9CM in 0.5369328520027921 sec."]

I, [2019-11-20T16:13:03.134026 #31955]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-20T20:11:36.564863 #4136]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-20T20:11:36.566836 #4136]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-20T20:11:36.568302 #4136]  INFO -- : ["Indexing ontology terms: ICD9CM..."]

I, [2019-11-20T20:11:36.571399 #4136]  INFO -- : ["Removed ontology terms index (0.002999925s)"]

I, [2019-11-20T20:11:37.286657 #4136]  INFO -- : ["Thread 1: Page 1 of 23 - 1000 ontology terms retrieved in 9.314e-06 sec."]

I, [2019-11-20T20:11:37.711825 #4136]  INFO -- : ["Thread 1: Page 1 of 23 attributes mapped in 0.425042061 sec."]

I, [2019-11-20T20:11:43.021195 #4136]  INFO -- : ["Thread 1: Page 1 of 23 - 1000 ontology terms indexed in 5.309235169 sec."]

I, [2019-11-20T20:11:43.318299 #4136]  INFO -- : ["Thread 1: Page 2 of 23 - 1000 ontology terms retrieved in 7.702e-06 sec."]

I, [2019-11-20T20:11:43.717223 #4136]  INFO -- : ["Thread 1: Page 2 of 23 attributes mapped in 0.3987852 sec."]

I, [2019-11-20T20:11:47.257259 #4136]  INFO -- : ["Thread 1: Page 2 of 23 - 1000 ontology terms indexed in 3.539898231 sec."]

I, [2019-11-20T20:11:47.637729 #4136]  INFO -- : ["Thread 1: Page 3 of 23 - 1000 ontology terms retrieved in 7.807e-06 sec."]

I, [2019-11-20T20:11:48.035452 #4136]  INFO -- : ["Thread 1: Page 3 of 23 attributes mapped in 0.397590107 sec."]

I, [2019-11-20T20:11:52.517272 #4136]  INFO -- : ["Thread 1: Page 3 of 23 - 1000 ontology terms indexed in 4.481687324 sec."]

I, [2019-11-20T20:11:52.826059 #4136]  INFO -- : ["Thread 1: Page 4 of 23 - 1000 ontology terms retrieved in 7.898e-06 sec."]

I, [2019-11-20T20:11:53.288983 #4136]  INFO -- : ["Thread 1: Page 4 of 23 attributes mapped in 0.462805321 sec."]

I, [2019-11-20T20:11:58.440014 #4136]  INFO -- : ["Thread 1: Page 4 of 23 - 1000 ontology terms indexed in 5.150904513 sec."]

I, [2019-11-20T20:11:58.737745 #4136]  INFO -- : ["Thread 1: Page 5 of 23 - 1000 ontology terms retrieved in 7.52e-06 sec."]

I, [2019-11-20T20:11:59.117082 #4136]  INFO -- : ["Thread 1: Page 5 of 23 attributes mapped in 0.379216746 sec."]

I, [2019-11-20T20:12:04.421169 #4136]  INFO -- : ["Thread 1: Page 5 of 23 - 1000 ontology terms indexed in 5.30395364 sec."]

I, [2019-11-20T20:12:04.717403 #4136]  INFO -- : ["Thread 1: Page 6 of 23 - 1000 ontology terms retrieved in 8.644e-06 sec."]

I, [2019-11-20T20:12:05.183420 #4136]  INFO -- : ["Thread 1: Page 6 of 23 attributes mapped in 0.465876926 sec."]

I, [2019-11-20T20:12:09.664103 #4136]  INFO -- : ["Thread 1: Page 6 of 23 - 1000 ontology terms indexed in 4.480550871 sec."]

I, [2019-11-20T20:12:09.961466 #4136]  INFO -- : ["Thread 1: Page 7 of 23 - 1000 ontology terms retrieved in 8.058e-06 sec."]

I, [2019-11-20T20:12:10.342308 #4136]  INFO -- : ["Thread 1: Page 7 of 23 attributes mapped in 0.380714738 sec."]

I, [2019-11-20T20:12:15.686432 #4136]  INFO -- : ["Thread 1: Page 7 of 23 - 1000 ontology terms indexed in 5.343938195 sec."]

I, [2019-11-20T20:12:16.129233 #4136]  INFO -- : ["Thread 1: Page 8 of 23 - 1000 ontology terms retrieved in 7.029e-06 sec."]

I, [2019-11-20T20:12:16.582026 #4136]  INFO -- : ["Thread 1: Page 8 of 23 attributes mapped in 0.452667702 sec."]

I, [2019-11-20T20:12:20.792814 #4136]  INFO -- : ["Thread 1: Page 8 of 23 - 1000 ontology terms indexed in 4.210656183 sec."]

I, [2019-11-20T20:12:21.087513 #4136]  INFO -- : ["Thread 1: Page 9 of 23 - 1000 ontology terms retrieved in 7.219e-06 sec."]

I, [2019-11-20T20:12:21.469819 #4136]  INFO -- : ["Thread 1: Page 9 of 23 attributes mapped in 0.382179132 sec."]

I, [2019-11-20T20:12:26.613627 #4136]  INFO -- : ["Thread 1: Page 9 of 23 - 1000 ontology terms indexed in 5.143680586 sec."]

I, [2019-11-20T20:12:26.985855 #4136]  INFO -- : ["Thread 1: Page 10 of 23 - 1000 ontology terms retrieved in 7.782e-06 sec."]

I, [2019-11-20T20:12:27.380387 #4136]  INFO -- : ["Thread 1: Page 10 of 23 attributes mapped in 0.394396125 sec."]

I, [2019-11-20T20:12:32.467134 #4136]  INFO -- : ["Thread 1: Page 10 of 23 - 1000 ontology terms indexed in 5.086608715 sec."]

I, [2019-11-20T20:12:32.767877 #4136]  INFO -- : ["Thread 1: Page 11 of 23 - 1000 ontology terms retrieved in 7.97e-06 sec."]

I, [2019-11-20T20:12:33.223928 #4136]  INFO -- : ["Thread 1: Page 11 of 23 attributes mapped in 0.455938289 sec."]

I, [2019-11-20T20:12:38.305496 #4136]  INFO -- : ["Thread 1: Page 11 of 23 - 1000 ontology terms indexed in 5.081417342 sec."]

I, [2019-11-20T20:12:38.598877 #4136]  INFO -- : ["Thread 1: Page 12 of 23 - 1000 ontology terms retrieved in 2.2769e-05 sec."]

I, [2019-11-20T20:12:38.982798 #4136]  INFO -- : ["Thread 1: Page 12 of 23 attributes mapped in 0.383776291 sec."]

I, [2019-11-20T20:12:44.133208 #4136]  INFO -- : ["Thread 1: Page 12 of 23 - 1000 ontology terms indexed in 5.15027603 sec."]

I, [2019-11-20T20:12:44.431718 #4136]  INFO -- : ["Thread 1: Page 13 of 23 - 1000 ontology terms retrieved in 7.666e-06 sec."]

I, [2019-11-20T20:12:44.884359 #4136]  INFO -- : ["Thread 1: Page 13 of 23 attributes mapped in 0.452523742 sec."]

I, [2019-11-20T20:12:50.032702 #4136]  INFO -- : ["Thread 1: Page 13 of 23 - 1000 ontology terms indexed in 5.148182598 sec."]

I, [2019-11-20T20:12:50.326437 #4136]  INFO -- : ["Thread 1: Page 14 of 23 - 1000 ontology terms retrieved in 7.397e-06 sec."]

I, [2019-11-20T20:12:50.708807 #4136]  INFO -- : ["Thread 1: Page 14 of 23 attributes mapped in 0.382245297 sec."]

I, [2019-11-20T20:12:54.930318 #4136]  INFO -- : ["Thread 1: Page 14 of 23 - 1000 ontology terms indexed in 4.221378079 sec."]

I, [2019-11-20T20:12:55.294632 #4136]  INFO -- : ["Thread 1: Page 15 of 23 - 1000 ontology terms retrieved in 7.357e-06 sec."]

I, [2019-11-20T20:12:55.712896 #4136]  INFO -- : ["Thread 1: Page 15 of 23 attributes mapped in 0.418134964 sec."]

I, [2019-11-20T20:12:59.829804 #4136]  INFO -- : ["Thread 1: Page 15 of 23 - 1000 ontology terms indexed in 4.116779637 sec."]

I, [2019-11-20T20:13:00.111839 #4136]  INFO -- : ["Thread 1: Page 16 of 23 - 1000 ontology terms retrieved in 8.059e-06 sec."]

I, [2019-11-20T20:13:00.494193 #4136]  INFO -- : ["Thread 1: Page 16 of 23 attributes mapped in 0.382237913 sec."]

I, [2019-11-20T20:13:05.525065 #4136]  INFO -- : ["Thread 1: Page 16 of 23 - 1000 ontology terms indexed in 5.030741553 sec."]

I, [2019-11-20T20:13:05.814767 #4136]  INFO -- : ["Thread 1: Page 17 of 23 - 1000 ontology terms retrieved in 8.038e-06 sec."]

I, [2019-11-20T20:13:06.272931 #4136]  INFO -- : ["Thread 1: Page 17 of 23 attributes mapped in 0.458039163 sec."]

I, [2019-11-20T20:13:11.401688 #4136]  INFO -- : ["Thread 1: Page 17 of 23 - 1000 ontology terms indexed in 5.128616587 sec."]

I, [2019-11-20T20:13:11.699502 #4136]  INFO -- : ["Thread 1: Page 18 of 23 - 1000 ontology terms retrieved in 8.085e-06 sec."]

I, [2019-11-20T20:13:12.076179 #4136]  INFO -- : ["Thread 1: Page 18 of 23 attributes mapped in 0.376560112 sec."]

I, [2019-11-20T20:13:17.163312 #4136]  INFO -- : ["Thread 1: Page 18 of 23 - 1000 ontology terms indexed in 5.08700241 sec."]

I, [2019-11-20T20:13:17.542588 #4136]  INFO -- : ["Thread 1: Page 19 of 23 - 1000 ontology terms retrieved in 7.175e-06 sec."]

I, [2019-11-20T20:13:17.933093 #4136]  INFO -- : ["Thread 1: Page 19 of 23 attributes mapped in 0.390386073 sec."]

I, [2019-11-20T20:13:23.079708 #4136]  INFO -- : ["Thread 1: Page 19 of 23 - 1000 ontology terms indexed in 5.146483593 sec."]

I, [2019-11-20T20:13:23.392047 #4136]  INFO -- : ["Thread 1: Page 20 of 23 - 1000 ontology terms retrieved in 2.0073e-05 sec."]

I, [2019-11-20T20:13:23.847937 #4136]  INFO -- : ["Thread 1: Page 20 of 23 attributes mapped in 0.45577553 sec."]

I, [2019-11-20T20:13:28.062454 #4136]  INFO -- : ["Thread 1: Page 20 of 23 - 1000 ontology terms indexed in 4.214362135 sec."]

I, [2019-11-20T20:13:28.381181 #4136]  INFO -- : ["Thread 1: Page 21 of 23 - 1000 ontology terms retrieved in 8.808e-06 sec."]

I, [2019-11-20T20:13:28.765370 #4136]  INFO -- : ["Thread 1: Page 21 of 23 attributes mapped in 0.384048986 sec."]

I, [2019-11-20T20:13:32.948961 #4136]  INFO -- : ["Thread 1: Page 21 of 23 - 1000 ontology terms indexed in 4.183444656 sec."]

I, [2019-11-20T20:13:33.278117 #4136]  INFO -- : ["Thread 1: Page 22 of 23 - 1000 ontology terms retrieved in 8.094e-06 sec."]

I, [2019-11-20T20:13:33.693673 #4136]  INFO -- : ["Thread 1: Page 22 of 23 attributes mapped in 0.415398305 sec."]

I, [2019-11-20T20:13:38.813819 #4136]  INFO -- : ["Thread 1: Page 22 of 23 - 1000 ontology terms indexed in 5.120012623 sec."]

I, [2019-11-20T20:13:38.964477 #4136]  INFO -- : ["Thread 1: Page 23 of 23 - 533 ontology terms retrieved in 1.6697e-05 sec."]

I, [2019-11-20T20:13:39.160596 #4136]  INFO -- : ["Thread 1: Page 23 of 23 attributes mapped in 0.195999767 sec."]

I, [2019-11-20T20:13:40.870177 #4136]  INFO -- : ["Thread 1: Page 23 of 23 - 533 ontology terms indexed in 1.709450258 sec."]

I, [2019-11-20T20:13:41.191821 #4136]  INFO -- : ["Ontology terms index commit in 0.320092853 sec."]

I, [2019-11-20T20:13:41.191894 #4136]  INFO -- : ["Completed indexing ontology terms: ICD9CM in 124.62434338399908 sec. 22533 classes."]

I, [2019-11-20T20:13:41.652636 #4136]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-20T20:13:41.674645 #4136] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 125.19s"]

I, [2019-11-20T20:13:41.696908 #4136]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-20T20:13:41.696961 #4136]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-20T20:13:42.079889 #4136]  INFO -- : ["Finished report for ICD9CM in 0.38281066800118424 sec."]

I, [2019-11-20T20:13:42.109694 #4136]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-22T09:22:59.777609 #4530]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-22T09:22:59.806371 #4530]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-22T09:22:59.807427 #4530]  INFO -- : ["Indexing ontology properties: ICD9CM..."]

I, [2019-11-22T09:22:59.812730 #4530]  INFO -- : ["Removed ontology properties index in 0.005202039 seconds."]

I, [2019-11-22T09:22:59.874988 #4530]  INFO -- : ["Indexing a total of 1 pages of 2500 properties each."]

I, [2019-11-22T09:22:59.891157 #4530]  INFO -- : ["Page 1 of ontology properties indexed in 0.016005195 seconds."]

I, [2019-11-22T09:22:59.954055 #4530]  INFO -- : ["Ontology properties index commit in 0.062722131 seconds."]

I, [2019-11-22T09:22:59.954144 #4530]  INFO -- : ["Completed indexing ontology properties of ICD9CM in 0.1467344599950593 sec. Total of 8 properties indexed."]

I, [2019-11-22T09:23:00.091629 #4530]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-22T09:23:00.109962 #4530] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 0.4s"]

I, [2019-11-22T09:23:00.137313 #4530]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-22T09:23:00.137502 #4530]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-22T09:23:00.673691 #4530]  INFO -- : ["Finished report for ICD9CM in 0.5360060890088789 sec."]

I, [2019-11-22T09:23:00.708615 #4530]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-25T08:28:13.675806 #22827]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-25T08:28:14.136566 #22827]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-25T08:28:14.137486 #22827]  INFO -- : ["metrics_for_submission start"]

I, [2019-11-25T08:28:17.675200 #22827]  INFO -- : ["Metrics groupby_children retrieved 4003 in 2.970041623 sec."]

I, [2019-11-25T08:28:17.679863 #22827]  INFO -- : ["Metrics count_classes retrieved 22533 in 0.001287805 sec."]

I, [2019-11-25T08:28:17.724915 #22827]  INFO -- : ["Metrics count cls with def 0 in 0.04488979 sec."]

I, [2019-11-25T08:28:17.725485 #22827]  INFO -- : ["Class metrics finished in 3.587907572 sec."]

I, [2019-11-25T08:28:17.725559 #22827]  INFO -- : ["class_metrics finished"]

I, [2019-11-25T08:28:17.726464 #22827]  INFO -- : ["individuals finished"]

I, [2019-11-25T08:28:17.727092 #22827]  INFO -- : ["properties finished"]

I, [2019-11-25T08:28:17.728468 #22827]  INFO -- : ["generation of metrics file finished"]

I, [2019-11-25T08:28:17.942706 #22827]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-25T08:28:17.966375 #22827] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 4.37s"]

I, [2019-11-25T08:28:17.998213 #22827]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-25T08:28:17.998271 #22827]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-25T08:28:19.211257 #22827]  INFO -- : ["Finished report for ICD9CM in 1.212825389986392 sec."]

I, [2019-11-25T08:28:19.238956 #22827]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-25T13:38:12.716091 #23269]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-25T13:38:12.718240 #23269]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-25T13:38:12.719035 #23269]  INFO -- : ["metrics_for_submission start"]

I, [2019-11-25T13:38:15.210555 #23269]  INFO -- : ["Metrics groupby_children retrieved 4003 in 2.333433781 sec."]

I, [2019-11-25T13:38:15.212802 #23269]  INFO -- : ["Metrics count_classes retrieved 22533 in 0.000721598 sec."]

I, [2019-11-25T13:38:15.259598 #23269]  INFO -- : ["Metrics count cls with def 0 in 0.046685473 sec."]

I, [2019-11-25T13:38:15.259868 #23269]  INFO -- : ["Class metrics finished in 2.54077709 sec."]

I, [2019-11-25T13:38:15.259903 #23269]  INFO -- : ["class_metrics finished"]

I, [2019-11-25T13:38:15.260510 #23269]  INFO -- : ["individuals finished"]

I, [2019-11-25T13:38:15.260907 #23269]  INFO -- : ["properties finished"]

I, [2019-11-25T13:38:15.262034 #23269]  INFO -- : ["generation of metrics file finished"]

I, [2019-11-25T13:38:15.444462 #23269]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-25T13:38:15.463127 #23269] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 2.87s"]

I, [2019-11-25T13:38:15.494895 #23269]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-25T13:38:15.494949 #23269]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-25T13:38:15.837981 #23269]  INFO -- : ["Finished report for ICD9CM in 0.3428925919579342 sec."]

I, [2019-11-25T13:38:15.878180 #23269]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-25T14:16:42.110970 #18107]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-25T14:16:42.113013 #18107]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-25T14:16:42.113724 #18107]  INFO -- : ["metrics_for_submission start"]

I, [2019-11-25T14:16:44.669191 #18107]  INFO -- : ["Metrics groupby_children retrieved 4003 in 2.42213605 sec."]

I, [2019-11-25T14:16:44.671206 #18107]  INFO -- : ["Metrics count_classes retrieved 22533 in 0.000753163 sec."]

I, [2019-11-25T14:16:44.711754 #18107]  INFO -- : ["Metrics count cls with def 0 in 0.040470732 sec."]

I, [2019-11-25T14:16:44.712006 #18107]  INFO -- : ["Class metrics finished in 2.59823014 sec."]

I, [2019-11-25T14:16:44.712035 #18107]  INFO -- : ["class_metrics finished"]

I, [2019-11-25T14:16:44.712528 #18107]  INFO -- : ["individuals finished"]

I, [2019-11-25T14:16:44.712881 #18107]  INFO -- : ["properties finished"]

I, [2019-11-25T14:16:44.714102 #18107]  INFO -- : ["generation of metrics file finished"]

I, [2019-11-25T14:16:44.915996 #18107]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-25T14:16:44.921450 #18107] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 2.89s"]

I, [2019-11-25T14:16:44.944086 #18107]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-25T14:16:44.944148 #18107]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-25T14:16:45.270937 #18107]  INFO -- : ["Finished report for ICD9CM in 0.3266836910042912 sec."]

I, [2019-11-25T14:16:45.295926 #18107]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /srv/ncbo/share/env/production/reports/ontologies_report.json.\n"]

I, [2019-11-25T14:54:50.272693 #28421]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/ICD9CM/submissions/17"]

I, [2019-11-25T14:54:50.274899 #28421]  INFO -- : ["Starting to process ICD9CM/submissions/17"]

I, [2019-11-25T14:54:50.275683 #28421]  INFO -- : ["metrics_for_submission start"]

I, [2019-11-25T14:54:54.132823 #28421]  INFO -- : ["Metrics groupby_children retrieved 4003 in 3.702764051 sec."]

I, [2019-11-25T14:54:54.136515 #28421]  INFO -- : ["Metrics count_classes retrieved 22533 in 0.00095404 sec."]

I, [2019-11-25T14:54:54.177817 #28421]  INFO -- : ["Metrics count cls with def 0 in 0.041111278 sec."]

I, [2019-11-25T14:54:54.178354 #28421]  INFO -- : ["Class metrics finished in 3.902588342 sec."]

I, [2019-11-25T14:54:54.178440 #28421]  INFO -- : ["class_metrics finished"]

I, [2019-11-25T14:54:54.179218 #28421]  INFO -- : ["individuals finished"]

I, [2019-11-25T14:54:54.179739 #28421]  INFO -- : ["properties finished"]

I, [2019-11-25T14:54:54.181056 #28421]  INFO -- : ["generation of metrics file finished"]

I, [2019-11-25T14:54:54.372733 #28421]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 completed successfully"]

D, [2019-11-25T14:54:54.402338 #28421] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/ICD9CM/submissions/17 in 4.2s"]

I, [2019-11-25T14:54:54.426482 #28421]  INFO -- : ["Running ontologies report for ontologies ICD9CM...\n"]

I, [2019-11-25T14:54:54.426553 #28421]  INFO -- : ["Processing report for ICD9CM - 1 of 1 ontologies."]

I, [2019-11-25T14:54:54.780427 #28421]  INFO -- : ["Finished report for ICD9CM in 0.3537290429812856 sec."]

I, [2019-11-25T14:54:54.803604 #28421]  INFO -- : ["Finished updating report for ontologies ICD9CM. Wrote report data to /




On Mar 6, 2020, at 2:41 PM, Koo, Jahoon <JAHOON.KOO at UCDENVER.EDU<mailto:JAHOON.KOO at UCDENVER.EDU>> wrote:

Hi BioPortal,

This is Jahoon, a student worker from Health Data Compass.

I am trying to migrate some UMLS ontologies from BioPortal to my virtual appliance.

I have succeeded to install UMLS installation, load subset (RRF) in MySQL, and generate RDF from MySQL as instructed. Currently, I have ttl files of UMLS ontologies that I want to migrate.
I have selected UMLS as the format for these ontologies and tried to upload ttl files through the BioPortal Web UI of my virtual appliance. However, I get errors from the Web UI saying, “Incomplete response received from application” or “We're sorry but something has gone wrong. We have been notified of this error” when I submit an ontology.

Could you please help me solving this problem?

Thank you.
Jahoon
_______________________________________________
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bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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