Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] search by id in a subtree

Madani, Sina Sina.Madani at vumc.org
Wed Feb 14 11:33:47 PST 2018


Hi,

I have another question while support is working on my previous one ☺
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?

Thanks!

From: Michael Dorf <mdorf at stanford.edu>
Date: Wednesday, January 31, 2018 at 6:05 PM
To: "support at bioontology.org" <support at bioontology.org>
Cc: "Madani, Sina" <Sina.Madani at vumc.org>
Subject: Fwd: [bioontology-support] search by id in a subtree

Hi,

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).
However, upon submitting a new ontology and after few seconds I get this error message in the web UI: “something went wrong”. Also, http://ontotoportal.admin<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> 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?
Scheduler.log or appliance.log doesn’t show any error either.

I re-tried the submission with a compressed tar file (72 Mb) too. This time,  http://ontotoportal.admin<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> 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
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?

Thanks!

Sina

I, [2018-01-28T11:19:17.181176 #3910]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/SNOMED/submissions/1"<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>]
I, [2018-01-28T11:19:17.219473 #3910]  INFO -- : ["Starting to process SNOMED/submissions/1"]
I, [2018-01-28T11:19:17.338663 #3910]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"]
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'"]



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180214/758f0855/attachment-0001.html>


More information about the bioontology-support mailing list